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Commit ed1db183 authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Add sample_metadata support from biomformat and example data

parent b9931fa0
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Showing with 755 additions and 34 deletions
.gitignore
View file @ ed1db183
......@@ -3,9 +3,7 @@
*.RData
.Rproj.user
*.Rproj
*.json
www/masque/doing/*
www/masque/todo/*
www/masque/done/*
www/masque/error/*
www/masque.png
\ No newline at end of file
www/masque.png
Rfunctions/Data_Management.R
View file @ ed1db183
......@@ -496,7 +496,7 @@ PercentAnnot <- function(counts,taxo)
}
## Get the counts and the taxo tables from the BIOM format file.
## Get the counts, the taxo and the target tables from the BIOM format file.
GetDataFromBIOM <-function(dataBIOM)
{
taxo = NULL
......@@ -515,14 +515,15 @@ GetDataFromBIOM <-function(dataBIOM)
counts = CheckCounts$counts
## Taxonomy table
tmp = observation_metadata(dataBIOM)
if(!is.null(tmp))
obs = observation_metadata(dataBIOM)
if(!is.null(obs))
{
if(is.data.frame(tmp)) taxo = as.data.frame(tmp)
if(!is.data.frame(tmp)) taxo = as.data.frame(t(sapply(observation_metadata(dataBIOM),FUN=function(x){x[1:7]})))
if(is.data.frame(obs)) taxo = as.data.frame(obs)
if(!is.data.frame(obs)) taxo = as.data.frame(t(sapply(observation_metadata(dataBIOM),FUN=function(x){x[1:7]})))
OTUnames = rownames(taxo)
## Modif taxo table (remove p__,... and change the colnames)
taxo_biom = taxo
taxo = as.data.frame(sapply(taxo,gsub,pattern="^.*__",replacement=""))
colnames(taxo) = c("Kingdom", "Phylum","Class","Order","Family","Genus","Species")
rownames(taxo) = OTUnames
......@@ -531,19 +532,34 @@ GetDataFromBIOM <-function(dataBIOM)
taxo[taxo=="Unassigned"] = NA
taxo=taxo[rowSums(is.na(taxo))!=dim(taxo)[2], ]
}
if(is.null(tmp) && !is.null(counts)) {taxo = data.frame(rownames(counts),row.names = rownames(counts));names(taxo)=NA; taxoCreated = TRUE}
## Sample metadata
target = sample_metadata(dataBIOM)
if(!is.null(target))
{
# Convert from list to dataframe
target = as.data.frame(target)
target$SampleID = rownames(target)
print(c(dim(target)[2], seq(1, dim(target)[2]-1)))
target = subset(target, select=c(dim(target)[2], seq(1, dim(target)[2]-1)))
}
print(target)
if(is.null(obs) && !is.null(counts)) {taxo = data.frame(rownames(counts),row.names = rownames(counts));names(taxo)=NA; taxoCreated = TRUE}
CheckTaxo = CheckTaxoTable(taxo,counts,taxoCreated)
#input the target file
#CheckTargetModel(,meta,)
## Pourcentage of annotation
tmp = PercentAnnot(counts,taxo)
perca = PercentAnnot(counts,taxo)
return(list(counts=counts,taxo=taxo,CheckCounts=CheckCounts,CheckTaxo=CheckTaxo,Percent=tmp$Percent,CheckPercent=tmp$Error))
return(list(counts=counts,taxo=taxo,taxo_biom=taxo_biom,target=target,CheckCounts=CheckCounts,CheckTaxo=CheckTaxo,Percent=perca$Percent,CheckPercent=perca$Error))
}
## Check the data
GetDataFromCT <-function(dataC,dataT, MGSTable)
{
l = c("k__", "p__", "c__", "o__", "f__", "g__", "s__")
## Counts table
counts = dataC
......@@ -554,11 +570,26 @@ GetDataFromCT <-function(dataC,dataT, MGSTable)
## Taxonomy table
taxo = as.data.frame(dataT)
CheckTaxo = CheckTaxoTable(taxo,counts, MGSTable)
# Biom taxonomy must have seven levels
taxo_temp = as.matrix(taxo)
if(dim(taxo_temp)[2] < 7){
taxo_temp = cbind(taxo_temp, matrix(NA, dim(taxo_temp)[1], 7 - dim(taxo_temp)[2]))
}
# All OTU must be referenced
if(dim(taxo_temp)[1] != dim(counts)[1]){
missing_elements = rownames(counts)[!rownames(counts) %in% rownames(taxo_temp)]
mat_missing = matrix(NA, length(missing_elements), dim(taxo_temp)[2])
rownames(mat_missing) = missing_elements
taxo_temp = rbind(taxo_temp, mat_missing)
}
taxo_biom = t(sapply(as.data.frame(t(taxo_temp)), FUN=function(x){paste(l,na.omit(x),sep="")}))
## Pourcentage of annotation
tmp = PercentAnnot(counts,taxo)
return(list(counts=counts,taxo=taxo,CheckCounts=CheckCounts,CheckTaxo=CheckTaxo,Percent=tmp$Percent,CheckPercent=tmp$Error))
return(list(counts=counts,taxo=taxo,taxo_biom = taxo_biom, CheckCounts=CheckCounts,CheckTaxo=CheckTaxo,Percent=tmp$Percent,CheckPercent=tmp$Error))
}
......
server.R
View file @ ed1db183
......@@ -16,7 +16,6 @@ shinyServer(function(input, output,session) {
file.create(namesfile,showWarnings=FALSE)
target = NULL
## JSON name for masque
curdir = getwd()
json_name = tempfile(pattern = "file", tmpdir = paste(curdir,"www","masque","todo",sep= .Platform$file.sep), fileext = ".json")
......@@ -257,6 +256,7 @@ shinyServer(function(input, output,session) {
Taxo = NULL
Counts = NULL
inputData = NULL
target = NULL
if(input$FileFormat=="fileCounts")
{
......@@ -267,7 +267,7 @@ shinyServer(function(input, output,session) {
if(!is.null(Counts) && !is.null(Taxo))
{
tmp = GetDataFromCT(Counts,Taxo, ifelse(input$TypeTable=="MGS" && input$FileFormat!="fileBiom", TRUE, FALSE))
data = list(counts=tmp$counts,taxo=tmp$taxo)
data = list(counts=tmp$counts,taxo=tmp$taxo, taxo_biom=tmp$taxo_biom)
## Remove row with only O
# data[["counts"]] = data[["counts"]][rowSums(data[["counts"]])>1,]
......@@ -282,12 +282,13 @@ shinyServer(function(input, output,session) {
if(!is.null(tmpBIOM))
{
tmp = GetDataFromBIOM(tmpBIOM)
data = list(counts=tmp$counts,taxo=tmp$taxo)
data = list(counts=tmp$counts,taxo=tmp$taxo, target=tmp$target, taxo_biom=tmp$taxo_biom)
## Remove row with only O
# data[["counts"]] = data[["counts"]][rowSums(data[["counts"]])>1,]
check = list(CheckCounts=tmp$CheckCounts,CheckTaxo=tmp$CheckTaxo,CheckPercent=tmp$CheckPercent)
percent = tmp$Percent
#if(!is.null(data$target)) values$TargetWorking = data$target
}
}
......@@ -720,12 +721,39 @@ shinyServer(function(input, output,session) {
## TARGET FILE
##
#####################################################
observe({
counts = dataInput()$data$counts
data = dataInput()$data$target
if(!is.null(data) && !is.null(counts))
{
names = colnames(data)
## Keep only the row which are in the count table
ind = which(rownames(data)%in%colnames(counts))
data = as.data.frame(data[ind,])
colnames(data) = names
## Replace "-" by "."
if(ncol(data)>1 && nrow(data)>1){
ind_num = which(sapply(as.data.frame(data[,-1]),is.numeric)) + 1
if(length(ind_num)>0){
data_tmp =cbind( as.data.frame(apply(as.data.frame(data[,-ind_num]),2,gsub,pattern = "-",replacement = ".")),data[,ind_num])
#data_tmp =cbind( as.data.frame(as.data.frame(data[,-ind_num])),data[,ind_num])
colnames(data_tmp) = c(colnames(data)[-ind_num],colnames(data)[ind_num])
data = data_tmp
}
if(length(ind_num)==0){data = as.data.frame(apply(data,2,gsub,pattern = "-",replacement = "."))}
}
values$TargetWorking = data
values$labeled = length(ind)/length(colnames(counts))*100.0
}
})
## Load target file
observe({
inFile <- input$fileTarget
#values$TargetWorking = NULL
counts = dataInput()$data$counts
labeled = 0
data = NULL
......@@ -760,7 +788,6 @@ shinyServer(function(input, output,session) {
}
if(length(ind_num)==0){data = as.data.frame(apply(data,2,gsub,pattern = "-",replacement = "."))}
}
values$TargetWorking = as.data.frame(data)
# ind_sel = Target_selection()
# if(length(ind))
......@@ -768,8 +795,8 @@ shinyServer(function(input, output,session) {
#ord = order(rownames(data))
#data = data[ord,]
### A SUPPRIMER
#rownames(data) <- colnames(counts)
### A SUqPPRIMER
#rownamQes(data) <- colnames(counts)
# Percent annotated
# print(ind)
......@@ -1370,9 +1397,21 @@ shinyServer(function(input, output,session) {
removeCssClass(class = 'pwdGREEN', selector = '#password')
}
})
# Run demo
observeEvent(input$DemoDataset, {
if(input$DemoDataset != "..."){
values$masque_key = input$DemoDataset
updateSelectInput(session, "FileFormat","",selected = "fileBiom")
reset("fileBiom")
reset("fileTree")
values$biom_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva.biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva_tree.nhx",sep=""),sep= .Platform$file.sep)
sendSweetAlert(messageId="DemoDataset", title = "Success", text = "Data of XXX were successfully loaded. You can go to statistical analysis section.", type = "success", html=TRUE)
}
})
## the same from home
observeEvent(input$Check_project_home,{
observeEvent(input$Check_project_home, {
values$masque_key = input$password_home
PS = Project_status(values$masque_key,values$curdir)
......@@ -1400,6 +1439,14 @@ shinyServer(function(input, output,session) {
})
# observeEvent(input$DemoDataset,{
# if(input$DemoDataset != "...")
# values$masque_key = input$DemoDataset
#
# PS = Project_status(values$masque_key,values$curdir)
# })
#eventReactive(input$refresh, {
# shinyjs::js$refresh()
#hideElement("gaugeMasque_progress")
......@@ -2022,22 +2069,40 @@ shinyServer(function(input, output,session) {
## Box for merged counts
output$BoxCountsMerge <- renderUI({
input$RunDESeq
#counts = isolate(dataMergeCounts()$counts)
# input$RunDESeq
# #counts = isolate(dataMergeCounts()$counts)
counts = isolate(dataMergeCounts()$CT_Norm)
taxo = input$TaxoSelect
#
# if(!is.null(counts) && taxo != "...")
# {
resDiff = ResDiffAnal()
int = input$Interaction2
if(!is.null(counts) && taxo != "...")
{
if(!is.null(resDiff)){
box(title=paste("Count table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
DT::dataTableOutput("CountsMerge"),
downloadButton('ExportCounts', 'Export normalised counts'),
downloadButton('ExportCounts', 'Export normalized counts'),
downloadButton('ExportRelative', 'Export relative abundance')
)
}
})
output$ButtonBiom <- renderUI({
resDiff = ResDiffAnal()
int = input$Interaction2
if(!is.null(resDiff)) downloadButton('ExportBiom', 'Export BIOM')
})
output$ExportBiom <- downloadHandler(
filename = function() { 'SHAMAN_data.biom' },
#write_biom doesn't handle properly the sample metadata
content = function(file){
write_biom(make_biom(dataMergeCounts()$CT_noNorm, sample_metadata=values$TargetWorking[,-1],
observation_metadata=dataInput()$data$taxo_biom), file)}
)
## Export in .csv
output$ExportCounts <- downloadHandler(
filename = function() { 'NormCounts.csv' },
......@@ -2048,7 +2113,8 @@ shinyServer(function(input, output,session) {
## Export in .csv
output$ExportRelative <- downloadHandler(
filename = function() { 'RelativeAb.csv' },
content = function(file){write.csv(sweep(round(counts(ResDiffAnal()$dds,normalized=TRUE)),2,colSums(round(counts(ResDiffAnal()$dds,normalized=TRUE))),`/`), file)}
content = function(file){write.csv(sweep(round(counts(ResDiffAnal()$dds,normalized=TRUE)),2,
colSums(round(counts(ResDiffAnal()$dds,normalized=TRUE))),`/`), file)}
)
## Export size factors
......@@ -4299,13 +4365,10 @@ shinyServer(function(input, output,session) {
observe({
taxo = input$TaxoSelect
target=values$TargetWorking
if(is.null(target) || is.null(taxo)) shinyjs::disable("AddFilter")
else if (is.null(target) || taxo =="...") shinyjs::disable("AddFilter")
else shinyjs::enable("AddFilter")
if(is.null(target) || taxo =="...")
{
shinyjs::disable("AddFilter")
} else {
shinyjs::enable("AddFilter")
}
})
###########
......
ui.R
View file @ ed1db183
......@@ -59,7 +59,7 @@ function(request) {
tabPanel("Authors", h3("The main contributors to SHAMAN:"),
p(a("Stevenn Volant", href="mailto:stevenn.volant@pasteur.fr"), "(Initiator, coding, testing, documentation, evaluation)"),
p(a("Amine Ghozlane",href="mailto:amine.ghozlane@pasteur.fr"), "(Coding, testing, documentation, evaluation, packaging)"),
p("Perrine Woringer", "(Coding, testing, Documentation)"),
p("Perrine Woringer", "(Coding, testing, documentation, feature suggestions)"),
p("Pierre Lechat", "(Coding, testing, feature suggestions)"),
h3("Acknowledgements"),
p("Thanks to the following people for patches and other suggestions for improvements:"),
......@@ -518,7 +518,9 @@ function(request) {
# selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Saved project"="fileRData"),selected="fileCounts"),
selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Project number"="projnum"),selected="fileCounts"),
conditionalPanel(condition="input.FileFormat=='fileCounts'",
checkboxInput("NoTaxoFile","No taxonomy table",value=FALSE)
checkboxInput("NoTaxoFile","No taxonomy table",value=FALSE),
selectInput("DemoDataset",h6(strong('Or select a dataset')),c("..."="...","ZymoBIOMICS mock 16S"="30a47fca2dc3"),selected="..."),
receiveSweetAlert(messageId = "DemoDataset")
),
conditionalPanel(condition="input.FileFormat=='projnum'",
inlineCSS(list(.pwdGREEN = "background-color: #DDF0B3",.pwdRED = "background-color: #F0B2AD")),
......@@ -619,6 +621,8 @@ function(request) {
column(width=6,uiOutput("SelectInteraction2"))
),
fluidRow(
column(width=6,uiOutput('ButtonBiom')),
#column(width=6,downloadButton('ExportBiom', 'Export BIOM')),
column(width=6,uiOutput("RunButton"))
)
),
......
www/masque/done/file30a47fca2dc3.json 0 → 100644
View file @ ed1db183
{"contaminant": "/tmp/Rtmpimkesv/file873bc712cf0_contaminant.fasta", "data_history_name": "data_shaman_37694_0", "paired": true, "host": "", "type": "16S", "pattern_R1": "_R1", "result_history_name": "shaman_37694_0", "path_R2": "/tmp/Rtmpimkesv/Masque_files_R2", "mail": "amine.ghozlane@pasteur.fr", "name": "file873bc712cf0", "path_R1": "/tmp/Rtmpimkesv/Masque_files_R1"}
\ No newline at end of file
www/masque/done/file30a47fca2dc3/shaman_greengenes.biom 0 → 100644
View file @ ed1db183
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:18:38","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_11","metadata":["k__Bacteria","p__Cyanobacteria","c__4C0d-2","o__MLE1-12","f__Bacteria","g__Cyanobacteria","s__4C0d-2"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Betaproteobacteria","o__Burkholderiales","f__Comamonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_17","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_18","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_19","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_2","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_20","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_21","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_22","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_23","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_24","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_25","metadata":["k__Bacteria","p__Bacteroidetes","c__Bacteroidia","o__Bacteroidales","f__S24-7","g__Bacteria","s__Bacteroidetes"]},{"id":"OTU_26","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_27","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_28","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Bacteria","s__Proteobacteria"]},{"id":"OTU_29","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_3","metadata":["k__Bacteria","p__Actinobacteria","c__Actinobacteria","o__Actinomycetales","f__Propionibacteriaceae","g__Propionibacterium","s__acnes"]},{"id":"OTU_30","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_31","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Lactobacillaceae","g__Lactobacillus","s__Bacteria"]},{"id":"OTU_32","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Bacillaceae","g__Bacillus","s__Bacteria"]},{"id":"OTU_33","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_34","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_35","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_36","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_37","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_38","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Pseudomonadales","f__Pseudomonadaceae","g__Pseudomonas","s__Bacteria"]},{"id":"OTU_39","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_4","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__aureus"]},{"id":"OTU_40","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_41","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__enterica"]},{"id":"OTU_42","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Bacteria","s__Firmicutes"]},{"id":"OTU_43","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_44","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Lactobacillales","f__Enterococcaceae","g__Enterococcus","s__Bacteria"]},{"id":"OTU_45","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_46","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_47","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_48","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_49","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_5","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_50","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_51","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_52","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_53","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_54","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_55","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_56","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_57","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_58","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_59","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_6","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_60","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_61","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_62","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_63","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_7","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_8","metadata":["k__","p__","c__","o__","f__","g__","s__"]},{"id":"OTU_9","metadata":["k__","p__","c__","o__","f__","g__","s__"]}],"columns":[{"id":"1ng.25cycles.1_S38_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.2_S39_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.25cycles.3_S40_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"25cycles"}},{"id":"1ng.30cycles.1_S50_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.2_S51_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"1ng.30cycles.3_S52_L001_001","metadata":{"StartDNA":"1ng","CyclePCR":"30cycles"}},{"id":"20ng.20cycles.1_S14_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.2_S15_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.20cycles.3_S16_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"20cycles"}},{"id":"20ng.25cycles.1_S2_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.2_S3_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"20ng.25cycles.3_S4_L001_001","metadata":{"StartDNA":"20ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.1_S26_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.2_S27_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"5ng.25cycles.3_S28_L001_001","metadata":{"StartDNA":"5ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.1_S62_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.2_S63_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.25cycles.3_S64_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"25cycles"}},{"id":"zero5ng.30cycles.1_S74_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.2_S75_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}},{"id":"zero5ng.30cycles.3_S76_L001_001","metadata":{"StartDNA":"05ng","CyclePCR":"30cycles"}}],"data":[[17452,27133,22628,34080,44295,26503,37448,44573,39161,39050,32932,40607,25728,29573,31779,37086,38992,27499,43560,25485,6836],[13,0,12,22,3,5,18,18,11,24,1,12,37,0,22,22,4,16,43,8,3],[2,1,3,28,1,2,10,11,1,11,8,8,16,6,20,5,1,9,10,13,3],[11,29,14,55,74,41,35,48,20,45,75,62,49,65,41,18,43,19,52,52,4],[20,40,34,76,116,38,35,70,51,70,113,79,32,74,72,43,64,24,77,48,5],[0,6,3,8,9,8,0,0,0,0,0,0,0,3,0,12,18,5,13,6,0],[23,62,30,79,149,57,39,72,59,86,106,100,62,47,51,51,67,34,63,90,10],[0,2,0,4,4,0,6,3,2,5,3,1,1,2,6,1,0,2,9,5,0],[5,0,0,4,4,0,0,1,2,4,0,7,5,1,1,0,0,1,5,0,0],[3,1,0,14,4,0,4,4,9,2,6,4,6,5,3,1,0,1,8,5,2],[1,4,3,10,4,2,0,0,1,0,0,0,0,2,1,14,6,1,15,5,3],[15860,23646,22078,29667,43537,24072,36479,47320,38806,32012,25103,30496,26135,34793,32500,38523,42830,30774,39737,28634,4774],[0,0,0,0,5,1,1,0,2,1,0,5,4,0,0,0,1,1,7,0,0],[13,23,11,54,78,31,13,60,44,66,66,57,22,51,53,22,33,17,61,37,5],[10,17,12,34,56,32,14,23,18,55,38,49,20,36,16,13,32,6,53,21,7],[0,1,0,4,1,1,0,0,0,2,1,1,7,0,1,3,3,0,2,4,0],[0,0,0,3,0,2,0,3,7,2,0,0,4,0,1,3,0,0,2,2,0],[18,42,20,68,88,57,37,48,35,86,90,68,52,80,65,32,59,20,80,61,11],[1,1,1,7,1,0,0,0,1,0,0,0,5,1,0,2,2,0,3,1,0],[1,0,1,1,0,0,0,3,1,1,1,0,0,3,2,0,0,2,0,0,0],[0,0,0,2,0,1,0,0,0,0,0,1,0,2,0,1,0,0,1,2,0],[1,0,0,0,0,1,4,1,2,3,0,1,1,4,0,1,2,1,7,6,1],[13125,22105,17509,23529,36814,19721,30956,43056,33082,25061,23471,26121,20873,27980,28509,32630,38907,27115,30649,23025,3775],[2,3,0,2,0,2,1,2,0,1,0,1,0,0,0,0,0,2,2,0,0],[1,0,0,2,2,0,0,0,0,2,2,1,0,1,1,0,0,1,4,0,0],[31,67,36,143,204,64,86,131,66,124,135,114,86,116,117,74,109,60,189,86,20],[111,221,114,414,591,245,197,336,241,391,448,394,231,379,317,186,311,109,506,319,61],[0,1,0,0,1,0,0,2,0,0,3,0,2,2,1,2,2,0,2,1,0],[0,0,0,0,3,0,4,1,0,2,0,2,0,0,0,0,0,0,2,0,0],[0,0,0,0,1,0,0,0,0,0,0,0,2,2,0,0,0,0,4,2,0],[1,3,2,4,7,1,5,0,0,0,2,0,0,1,5,1,3,1,2,4,0],[225,379,195,805,1014,423,387,669,422,858,826,711,406,628,505,341,511,249,1032,668,30],[5,2,1,1,4,3,0,0,0,4,1,0,2,3,4,0,0,0,5,0,0],[13337,23359,16051,28762,41768,20948,35150,39582,31692,31582,26212,25297,25494,32339,34775,39042,38318,25859,39136,26583,2790],[0,0,5,2,0,0,0,2,2,1,0,2,0,0,0,2,0,0,3,0,0],[0,0,0,0,1,0,0,3,1,0,2,0,0,0,0,0,0,1,3,1,0],[2,4,1,16,15,8,2,4,5,33,28,9,9,5,8,4,1,0,20,15,3],[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,2,3,0,10,0],[195,379,163,976,1055,534,504,662,366,1009,867,564,595,730,708,421,503,222,1225,583,85],[76,149,84,320,410,129,150,252,132,329,309,278,162,237,190,101,194,94,409,240,22],[0,0,0,2,0,0,0,0,0,0,0,1,3,0,1,0,0,1,0,0,0],[0,0,2,0,0,1,0,0,0,1,0,2,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,2,0,0,0,0,0],[0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,6,1,1,5,2,0],[11531,20057,16044,23534,35804,15246,26747,35766,29197,26834,24773,29176,19939,27576,27496,27523,33651,24155,31504,22764,1540],[0,0,0,0,0,0,0,0,0,5,0,0,0,0,1,1,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0],[0,0,0,2,0,0,0,0,0,3,0,0,0,0,0,0,0,0,3,0,0],[0,0,1,2,0,0,3,3,3,1,1,1,5,2,0,1,0,0,6,3,0],[36,50,24,100,95,47,64,74,46,91,89,111,56,84,59,37,45,20,140,83,3],[249,450,266,1061,1311,492,477,712,443,1093,933,930,542,916,663,398,548,274,1285,737,49],[1,0,0,2,0,0,0,0,2,0,0,2,1,1,1,1,2,2,2,3,0],[41,59,27,171,185,84,54,91,74,173,163,170,95,90,127,30,76,61,200,139,10],[5,5,6,17,27,17,11,5,12,25,28,24,15,11,25,3,6,6,45,18,1],[1,0,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0,0,0,0],[8183,13707,10964,16276,24625,12822,18729,23977,19123,17982,17070,19830,13793,18802,17884,18929,23174,15187,21971,15719,2336],[17,44,12,101,137,71,36,100,59,94,86,118,59,90,71,46,51,32,122,72,17],[1,1,0,9,6,10,7,5,3,5,6,8,1,8,1,1,5,1,9,4,2],[3,3,2,42,29,14,1,9,1,37,24,16,3,15,7,5,1,1,25,12,2],[0,2,0,2,0,0,0,0,0,0,0,3,0,0,1,0,0,0,6,0,0],[6506,11883,8080,11966,19193,9309,14386,19327,15146,13448,12560,13118,9135,12995,13890,15038,18146,11681,15168,11666,2165],[5082,9047,7033,10887,16871,6722,12362,18325,14321,11921,11802,13621,9812,13294,13394,12133,15601,9962,15972,11023,651],[7,5,17,39,8,6,29,26,19,32,1,22,47,6,51,17,0,22,58,17,3]]}
\ No newline at end of file
www/masque/done/file30a47fca2dc3/shaman_greengenes_annotation.tsv 0 → 100644
View file @ ed1db183
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_15 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_58 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_36 Bacteria Cyanobacteria 4C0d-2 MLE1-12
OTU_4 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_23 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_14 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae
OTU_12 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_1 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_26 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_33 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_62 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_49 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae
OTU_44 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_60 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_13 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_55 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_21 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_43 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7
OTU_25 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_6 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_41 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae
OTU_2 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_19 Bacteria Actinobacteria Actinobacteria Actinomycetales Propionibacteriaceae Propionibacterium acnes
OTU_37 Bacteria Firmicutes Bacilli Bacillales Bacillaceae
OTU_22 Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus
OTU_42 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus
OTU_57 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_45 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_3 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_38 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_34 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
OTU_39 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_61 Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus aureus
OTU_5 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_31 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella enterica
OTU_32 Bacteria Firmicutes Bacilli Bacillales Listeriaceae
OTU_7 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
OTU_54 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus
www/masque/done/file30a47fca2dc3/shaman_otu.fasta 0 → 100644
View file @ ed1db183
This diff is collapsed.
www/masque/done/file30a47fca2dc3/shaman_otu_table.tsv 0 → 100644
View file @ ed1db183
#OTU ID 1ng-25cycles-1_S38_L001_001 1ng-25cycles-2_S39_L001_001 1ng-25cycles-3_S40_L001_001 1ng-30cycles-1_S50_L001_001 1ng-30cycles-2_S51_L001_001 1ng-30cycles-3_S52_L001_001 20ng-20cycles-1_S14_L001_001 20ng-20cycles-2_S15_L001_001 20ng-20cycles-3_S16_L001_001 20ng-25cycles-1_S2_L001_001 20ng-25cycles-2_S3_L001_001 20ng-25cycles-3_S4_L001_001 5ng-25cycles-1_S26_L001_001 5ng-25cycles-2_S27_L001_001 5ng-25cycles-3_S28_L001_001 zero5ng-25cycles-1_S62_L001_001 zero5ng-25cycles-2_S63_L001_001 zero5ng-25cycles-3_S64_L001_001 zero5ng-30cycles-1_S74_L001_001 zero5ng-30cycles-2_S75_L001_001 zero5ng-30cycles-3_S76_L001_001
OTU_1 17452 27133 22628 34080 44295 26503 37448 44573 39161 39050 32932 40607 25728 29573 31779 37086 38992 27499 43560 25485 6836
OTU_10 13 0 12 22 3 5 18 18 11 24 1 12 37 0 22 22 4 16 43 8 3
OTU_11 2 1 3 28 1 2 10 11 1 11 8 8 16 6 20 5 1 9 10 13 3
OTU_12 11 29 14 55 74 41 35 48 20 45 75 62 49 65 41 18 43 19 52 52 4
OTU_13 20 40 34 76 116 38 35 70 51 70 113 79 32 74 72 43 64 24 77 48 5
OTU_14 0 6 3 8 9 8 0 0 0 0 0 0 0 3 0 12 18 5 13 6 0
OTU_15 23 62 30 79 149 57 39 72 59 86 106 100 62 47 51 51 67 34 63 90 10
OTU_16 0 2 0 4 4 0 6 3 2 5 3 1 1 2 6 1 0 2 9 5 0
OTU_17 5 0 0 4 4 0 0 1 2 4 0 7 5 1 1 0 0 1 5 0 0
OTU_18 3 1 0 14 4 0 4 4 9 2 6 4 6 5 3 1 0 1 8 5 2
OTU_19 1 4 3 10 4 2 0 0 1 0 0 0 0 2 1 14 6 1 15 5 3
OTU_2 15860 23646 22078 29667 43537 24072 36479 47320 38806 32012 25103 30496 26135 34793 32500 38523 42830 30774 39737 28634 4774
OTU_20 0 0 0 0 5 1 1 0 2 1 0 5 4 0 0 0 1 1 7 0 0
OTU_21 13 23 11 54 78 31 13 60 44 66 66 57 22 51 53 22 33 17 61 37 5
OTU_22 10 17 12 34 56 32 14 23 18 55 38 49 20 36 16 13 32 6 53 21 7
OTU_23 0 1 0 4 1 1 0 0 0 2 1 1 7 0 1 3 3 0 2 4 0
OTU_24 0 0 0 3 0 2 0 3 7 2 0 0 4 0 1 3 0 0 2 2 0
OTU_25 18 42 20 68 88 57 37 48 35 86 90 68 52 80 65 32 59 20 80 61 11
OTU_26 1 1 1 7 1 0 0 0 1 0 0 0 5 1 0 2 2 0 3 1 0
OTU_27 1 0 1 1 0 0 0 3 1 1 1 0 0 3 2 0 0 2 0 0 0
OTU_28 0 0 0 2 0 1 0 0 0 0 0 1 0 2 0 1 0 0 1 2 0
OTU_29 1 0 0 0 0 1 4 1 2 3 0 1 1 4 0 1 2 1 7 6 1
OTU_3 13125 22105 17509 23529 36814 19721 30956 43056 33082 25061 23471 26121 20873 27980 28509 32630 38907 27115 30649 23025 3775
OTU_30 2 3 0 2 0 2 1 2 0 1 0 1 0 0 0 0 0 2 2 0 0
OTU_31 1 0 0 2 2 0 0 0 0 2 2 1 0 1 1 0 0 1 4 0 0
OTU_32 31 67 36 143 204 64 86 131 66 124 135 114 86 116 117 74 109 60 189 86 20
OTU_33 111 221 114 414 591 245 197 336 241 391 448 394 231 379 317 186 311 109 506 319 61
OTU_34 0 1 0 0 1 0 0 2 0 0 3 0 2 2 1 2 2 0 2 1 0
OTU_35 0 0 0 0 3 0 4 1 0 2 0 2 0 0 0 0 0 0 2 0 0
OTU_36 0 0 0 0 1 0 0 0 0 0 0 0 2 2 0 0 0 0 4 2 0
OTU_37 1 3 2 4 7 1 5 0 0 0 2 0 0 1 5 1 3 1 2 4 0
OTU_38 225 379 195 805 1014 423 387 669 422 858 826 711 406 628 505 341 511 249 1032 668 30
OTU_39 5 2 1 1 4 3 0 0 0 4 1 0 2 3 4 0 0 0 5 0 0
OTU_4 13337 23359 16051 28762 41768 20948 35150 39582 31692 31582 26212 25297 25494 32339 34775 39042 38318 25859 39136 26583 2790
OTU_40 0 0 5 2 0 0 0 2 2 1 0 2 0 0 0 2 0 0 3 0 0
OTU_41 0 0 0 0 1 0 0 3 1 0 2 0 0 0 0 0 0 1 3 1 0
OTU_42 2 4 1 16 15 8 2 4 5 33 28 9 9 5 8 4 1 0 20 15 3
OTU_43 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 10 0
OTU_44 195 379 163 976 1055 534 504 662 366 1009 867 564 595 730 708 421 503 222 1225 583 85
OTU_45 76 149 84 320 410 129 150 252 132 329 309 278 162 237 190 101 194 94 409 240 22
OTU_46 0 0 0 2 0 0 0 0 0 0 0 1 3 0 1 0 0 1 0 0 0
OTU_47 0 0 2 0 0 1 0 0 0 1 0 2 0 0 0 0 0 0 0 0 0
OTU_48 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 2 0 0 0 0 0
OTU_49 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 6 1 1 5 2 0
OTU_5 11531 20057 16044 23534 35804 15246 26747 35766 29197 26834 24773 29176 19939 27576 27496 27523 33651 24155 31504 22764 1540
OTU_50 0 0 0 0 0 0 0 0 0 5 0 0 0 0 1 1 0 0 0 0 0
OTU_51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0
OTU_52 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 0 0 0 3 0 0
OTU_53 0 0 1 2 0 0 3 3 3 1 1 1 5 2 0 1 0 0 6 3 0
OTU_54 36 50 24 100 95 47 64 74 46 91 89 111 56 84 59 37 45 20 140 83 3
OTU_55 249 450 266 1061 1311 492 477 712 443 1093 933 930 542 916 663 398 548 274 1285 737 49
OTU_56 1 0 0 2 0 0 0 0 2 0 0 2 1 1 1 1 2 2 2 3 0
OTU_57 41 59 27 171 185 84 54 91 74 173 163 170 95 90 127 30 76 61 200 139 10
OTU_58 5 5 6 17 27 17 11 5 12 25 28 24 15 11 25 3 6 6 45 18 1
OTU_59 1 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 0 0 0
OTU_6 8183 13707 10964 16276 24625 12822 18729 23977 19123 17982 17070 19830 13793 18802 17884 18929 23174 15187 21971 15719 2336
OTU_60 17 44 12 101 137 71 36 100 59 94 86 118 59 90 71 46 51 32 122 72 17
OTU_61 1 1 0 9 6 10 7 5 3 5 6 8 1 8 1 1 5 1 9 4 2
OTU_62 3 3 2 42 29 14 1 9 1 37 24 16 3 15 7 5 1 1 25 12 2
OTU_63 0 2 0 2 0 0 0 0 0 0 0 3 0 0 1 0 0 0 6 0 0
OTU_7 6506 11883 8080 11966 19193 9309 14386 19327 15146 13448 12560 13118 9135 12995 13890 15038 18146 11681 15168 11666 2165
OTU_8 5082 9047 7033 10887 16871 6722 12362 18325 14321 11921 11802 13621 9812 13294 13394 12133 15601 9962 15972 11023 651
OTU_9 7 5 17 39 8 6 29 26 19 32 1 22 47 6 51 17 0 22 58 17 3
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View file @ ed1db183
Type Count Mean_length Median_length
Amplicon 4248638 428 427
Dereplication 1629789 428 427
Singleton_removed 40537 429 427
Chimera_removed 34496 429 427
OTU 63 354 427
silva_annotation 39
greengenes_annotation 39
rdp_annotation 62
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sample Raw_reads_fwd Raw_mean_length_fwd Raw_median_length_fwd Raw_reads_rev Raw_mean_length_rev Raw_median_length_rev Trimmed Trimmed_fwd Trimmed_rev Removed Removed_fwd Removed_rev Filtered_reads_fwd Filtered_mean_length_fwd Filtered_median_length_fwd Filtered_reads_rev Filtered_mean_length_rev Filtered_median_length_rev Combined pairs Uncombined pairs Selected_dereplication Selected_singleton Selected_chimera Selected_otu Mapped_reads Mapping_percent_combined
5ng-25cycles-1_S26_L001_001 216807 300 301 216807 300 300 403438 196888 206550 27842 17587 10255 192017 265 277 192017 227 231 167270 192017 60409 1507 1277 5 153559 79.97
20ng-25cycles-1_S2_L001_001 302678 300 301 302678 300 300 560043 274679 285364 42410 25097 17313 265513 265 277 265513 224 229 228922 265513 90528 2208 1749 5 202669 76.33
1ng-30cycles-1_S50_L001_001 275152 300 301 275152 300 300 509447 250179 259268 37693 21809 15884 242096 265 277 242096 222 227 209033 242096 84557 1998 1542 7 183410 75.76
zero5ng-25cycles-1_S62_L001_001 308283 300 301 308283 300 300 569407 277786 291621 43427 26767 16660 270219 265 277 270219 225 230 233528 270219 82353 2133 1951 2 222829 82.46
1ng-25cycles-3_S40_L001_001 172137 300 301 172137 300 300 315854 154559 161295 26482 15642 10840 149233 265 277 149233 223 227 128265 149233 48587 1285 1172 1 121491 81.41
5ng-25cycles-3_S28_L001_001 285903 300 301 285903 300 300 531229 257695 273534 37412 25043 12369 252430 264 277 252430 229 234 220357 252430 77958 1986 1662 4 203446 80.6
zero5ng-25cycles-2_S63_L001_001 352123 300 301 352123 300 300 648535 318719 329816 50482 28176 22306 308459 267 277 308459 221 226 266924 308459 98469 2510 2256 2 252325 81.8
zero5ng-25cycles-3_S64_L001_001 236495 300 301 236495 300 300 437038 212481 224557 33097 21161 11936 207488 265 277 207488 227 232 180797 207488 62110 1659 1557 2 173561 83.65
zero5ng-30cycles-1_S74_L001_001 359368 300 301 359368 300 300 665454 326768 338686 49132 28451 20681 316575 266 277 316575 223 227 274564 316575 105773 2526 1974 7 243522 76.92
1ng-25cycles-2_S39_L001_001 225513 300 301 225513 300 300 410838 203514 207324 37100 18912 18188 193922 267 277 193922 218 217 165528 193922 67393 1678 1445 2 152993 78.89
20ng-20cycles-1_S14_L001_001 297586 300 301 297586 300 300 550934 268644 282290 40695 25399 15296 261634 265 277 261634 226 231 226892 261634 79872 2069 1860 3 214491 81.98
1ng-30cycles-3_S52_L001_001 256766 300 301 256766 300 300 453161 223254 229907 58344 31485 26859 206824 257 272 206824 208 205 154532 206824 86516 1969 1688 3 137773 66.61
20ng-25cycles-3_S4_L001_001 296908 300 301 296908 300 300 549201 268361 280840 41730 25666 16064 260316 265 277 260316 226 231 226248 260316 86241 2126 1726 2 202205 77.68
zero5ng-30cycles-2_S75_L001_001 242911 300 301 242911 300 300 449556 221480 228076 33397 18562 14835 213997 267 278 213997 222 227 186286 213997 69094 1759 1455 3 168284 78.64
20ng-25cycles-2_S3_L001_001 269896 300 301 269896 300 300 497132 245483 251649 39492 21246 18246 235824 267 277 235824 221 225 203843 235824 82805 2068 1612 4 178385 75.64
20ng-20cycles-3_S16_L001_001 306702 300 301 306702 300 300 567042 275507 291535 42771 27605 15166 269014 265 277 269014 228 233 234694 269014 80070 2038 1839 3 222691 82.78
zero5ng-30cycles-3_S76_L001_001 132333 300 301 132333 300 300 183132 106023 77109 80943 25722 55221 65823 247 263 65823 174 177 29501 65823 23219 370 323 1 25229 38.33
20ng-20cycles-2_S15_L001_001 386487 300 301 386487 300 300 714269 350082 364187 53920 31621 22299 339401 266 277 339401 223 228 293514 339401 106564 2767 2482 3 275380 81.14
1ng-30cycles-2_S51_L001_001 391843 300 301 391843 300 300 724875 357756 367119 53718 28996 24722 345232 267 277 345232 221 226 299176 345232 117753 2869 2373 3 268610 77.81
5ng-25cycles-2_S27_L001_001 284620 300 301 284620 300 300 528610 259384 269226 36853 21459 15394 252210 267 277 252210 224 229 219794 252210 80454 2038 1683 1 201061 79.72
1ng-25cycles-1_S38_L001_001 133794 300 301 133794 300 300 245147 120830 124317 20848 11371 9477 115918 265 277 115918 220 223 98970 115918 39064 974 870 0 92208 79.55
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OTU_1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 1.0 Lactobacillaceae family 1.0 Lactobacillus genus 1.0
OTU_2 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_3 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 1.0 Listeria genus 1.0
OTU_4 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.99 Bacillus genus 0.99
OTU_5 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 1.0
OTU_6 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Escherichia/Shigella genus 1.0
OTU_7 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 1.0 Enterococcaceae family 1.0 Enterococcus genus 1.0
OTU_8 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 Pseudomonadales order 1.0 Pseudomonadaceae family 1.0 Pseudomonas genus 1.0
OTU_9 - Root rootrank 1.0 Bacteria domain 0.86 Firmicutes phylum 0.12 Clostridia class 0.06 Halanaerobiales order 0.03 Halanaerobiaceae family 0.03 Halothermothrix genus 0.01
OTU_10 - Root rootrank 1.0 Bacteria domain 0.97 Firmicutes phylum 0.18 Negativicutes class 0.05 Selenomonadales order 0.05 Veillonellaceae family 0.05 Thermosinus genus 0.01
OTU_11 Root rootrank 1.0 Archaea domain 0.31 "Crenarchaeota" phylum 0.19 Thermoprotei class 0.19 Thermoproteales order 0.18 Thermoproteaceae family 0.18 Thermocladium genus 0.17
OTU_12 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Escherichia/Shigella genus 1.0
OTU_13 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 0.58
OTU_14 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Betaproteobacteria class 1.0 Burkholderiales order 1.0 Comamonadaceae family 1.0 Pelomonas genus 1.0
OTU_15 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 1.0 Listeria genus 1.0
OTU_16 - Root rootrank 1.0 Archaea domain 0.21 "Euryarchaeota" phylum 0.2 Thermoplasmata class 0.18 Methanomassiliicoccales order 0.18 Methanomassiliicoccaceae family 0.18 Methanomassiliicoccus genus 0.18
OTU_17 Root rootrank 1.0 Bacteria domain 0.82 "Bacteroidetes" phylum 0.42 "Bacteroidia" class 0.14 "Bacteroidales" order 0.14 "Bacteroidales"_incertae_sedis family 0.1 Phocaeicola genus 0.1
OTU_18 - Root rootrank 1.0 Archaea domain 0.23 Pacearchaeota phylum 0.05 Pacearchaeota Incertae Sedis AR13 genus 0.05
OTU_19 Root rootrank 1.0 Bacteria domain 1.0 "Actinobacteria" phylum 1.0 Actinobacteria class 1.0 Actinobacteridae subclass 1.0 Actinomycetales order 1.0 Propionibacterineae suborder 1.0 Propionibacteriaceae family 1.0 Propionibacterium genus 1.0
OTU_20 Root rootrank 1.0 Bacteria domain 0.94 "Synergistetes" phylum 0.11 Synergistia class 0.11 Synergistales order 0.11 Synergistaceae family 0.11 Jonquetella genus 0.09
OTU_21 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 Pseudomonadales order 1.0 Pseudomonadaceae family 1.0 Pseudomonas genus 0.74
OTU_22 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 0.99 Lactobacillales order 0.99 Lactobacillaceae family 0.97 Lactobacillus genus 0.97
OTU_23 - Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.99 Bacillus genus 0.99
OTU_24 - Root rootrank 1.0 Bacteria domain 0.74 "Deinococcus-Thermus" phylum 0.03 Deinococci class 0.03 Thermales order 0.03 Thermaceae family 0.03 Marinithermus genus 0.03
OTU_25 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Staphylococcaceae family 0.99 Staphylococcus genus 0.99
OTU_26 - Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 1.0 Lactobacillaceae family 1.0 Lactobacillus genus 1.0
OTU_27 Root rootrank 1.0 Bacteria domain 0.75 "Proteobacteria" phylum 0.33 Gammaproteobacteria class 0.28 Gammaproteobacteria_incertae_sedis order 0.19 Candidatus Carsonella genus 0.19
OTU_28 Root rootrank 1.0 Bacteria domain 0.99 "Planctomycetes" phylum 0.21 Planctomycetia class 0.21 Planctomycetales order 0.17 Planctomycetaceae family 0.17 Aquisphaera genus 0.07
OTU_29 Root rootrank 1.0 Bacteria domain 0.88 "Proteobacteria" phylum 0.32 Deltaproteobacteria class 0.09 Myxococcales order 0.07 Cystobacterineae suborder 0.05 Myxococcaceae family 0.01 Pyxidicoccus genus 0.0
OTU_30 Root rootrank 1.0 Bacteria domain 0.95 "Actinobacteria" phylum 0.07 Actinobacteria class 0.07 Coriobacteridae subclass 0.04 Coriobacteriales order 0.04 "Coriobacterineae" suborder 0.04 Coriobacteriaceae family 0.04 Adlercreutzia genus 0.01
OTU_31 - Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 1.0
OTU_32 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.98 Listeriaceae family 0.96 Listeria genus 0.96
OTU_33 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 0.99 Bacilli class 0.99 Lactobacillales order 0.99 Lactobacillaceae family 0.98 Lactobacillus genus 0.96
OTU_34 - Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 1.0 Listeria genus 1.0
OTU_35 Root rootrank 1.0 Bacteria domain 0.88 "Bacteroidetes" phylum 0.15 Cytophagia class 0.11 Cytophagales order 0.11 Cytophagaceae family 0.1 Nibribacter genus 0.08
OTU_36 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 0.96 Deltaproteobacteria class 0.95 Bdellovibrionales order 0.95 Bdellovibrionaceae family 0.95 Vampirovibrio genus 0.95
OTU_37 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.89 Bacillus genus 0.89
OTU_38 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Listeriaceae family 0.79 Listeria genus 0.79
OTU_39 - Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_40 Root rootrank 1.0 Archaea domain 0.4 "Euryarchaeota" phylum 0.24 Methanopyri class 0.1 Methanopyrales order 0.1 Methanopyraceae family 0.1 Methanopyrus genus 0.1
OTU_41 - Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Escherichia/Shigella genus 1.0
OTU_42 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Bacillaceae 2 family 0.81 Allobacillus genus 0.63
OTU_43 Root rootrank 1.0 Bacteria domain 1.0 "Bacteroidetes" phylum 1.0 "Bacteroidia" class 1.0 "Bacteroidales" order 1.0 "Porphyromonadaceae" family 0.98 Barnesiella genus 0.33
OTU_44 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.99 Staphylococcaceae family 0.76 Staphylococcus genus 0.75
OTU_45 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.78 Enterococcaceae family 0.6 Melissococcus genus 0.2
OTU_46 Root rootrank 1.0 Bacteria domain 0.88 "Bacteroidetes" phylum 0.29 "Bacteroidia" class 0.12 "Bacteroidales" order 0.12 "Bacteroidales"_incertae_sedis family 0.06 Phocaeicola genus 0.06
OTU_47 Root rootrank 1.0 Bacteria domain 0.97 Firmicutes phylum 0.27 Clostridia class 0.19 Clostridiales order 0.15 Peptococcaceae 2 family 0.04 Cryptanaerobacter genus 0.03
OTU_48 Root rootrank 1.0 Archaea domain 0.07 "Euryarchaeota" phylum 0.04 Thermoplasmata class 0.04 Methanomassiliicoccales order 0.04 Methanomassiliicoccaceae family 0.04 Methanomassiliicoccus genus 0.04
OTU_49 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Alphaproteobacteria class 1.0 Sphingomonadales order 1.0 Sphingomonadaceae family 1.0 Sphingomonas genus 1.0
OTU_50 Root rootrank 1.0 Bacteria domain 0.77 "Bacteroidetes" phylum 0.15 Cytophagia class 0.04 Cytophagales order 0.04 Cytophagaceae family 0.04 Persicitalea genus 0.02
OTU_51 Root rootrank 1.0 Bacteria domain 0.71 "Deinococcus-Thermus" phylum 0.08 Deinococci class 0.08 Thermales order 0.07 Thermaceae family 0.07 Vulcanithermus genus 0.05
OTU_52 - Root rootrank 1.0 Bacteria domain 0.9 "Spirochaetes" phylum 0.06 Spirochaetia class 0.06 Spirochaetales order 0.06 Spirochaetales_incertae_sedis family 0.04 Exilispira genus 0.04
OTU_53 Root rootrank 1.0 Bacteria domain 0.87 "Aquificae" phylum 0.12 Aquificae class 0.12 Desulfurobacteriales order 0.12 Desulfurobacteriaceae family 0.12 Balnearium genus 0.08
OTU_54 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.98 Enterococcaceae family 0.56 Enterococcus genus 0.31
OTU_55 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Bacillaceae 1 family 0.86 Bacillus genus 0.85
OTU_56 - Root rootrank 1.0 Bacteria domain 0.85 "Bacteroidetes" phylum 0.16 Cytophagia class 0.12 Cytophagales order 0.12 Cytophagaceae family 0.11 Persicitalea genus 0.08
OTU_57 Root rootrank 1.0 Bacteria domain 1.0 "Proteobacteria" phylum 1.0 Gammaproteobacteria class 1.0 "Enterobacteriales" order 1.0 Enterobacteriaceae family 1.0 Salmonella genus 0.79
OTU_58 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.81 Bacillaceae 2 family 0.67 Terribacillus genus 0.35
OTU_59 - Root rootrank 1.0 Bacteria domain 0.88 Firmicutes phylum 0.15 Clostridia class 0.07 Clostridiales order 0.07 Clostridiaceae 1 family 0.04 Proteiniclasticum genus 0.04
OTU_60 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 0.87 Listeriaceae family 0.87 Listeria genus 0.87
OTU_61 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Bacillales order 1.0 Staphylococcaceae family 1.0 Staphylococcus genus 1.0
OTU_62 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Bacilli class 1.0 Lactobacillales order 0.99 Lactobacillaceae family 0.97 Lactobacillus genus 0.96
OTU_63 - Root rootrank 1.0 Bacteria domain 0.96 "Aquificae" phylum 0.05 Aquificae class 0.05 Aquificales order 0.05 Hydrogenothermaceae family 0.05 Venenivibrio genus 0.05
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View file @ ed1db183
{"id":null,"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"biomformat 1.12.0","date":"2019-08-13 18:17:11","matrix_type":"dense","matrix_element_type":"int","shape":[63,21],"rows":[{"id":"OTU_1","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica"]},{"id":"OTU_10","metadata":["k__Bacteria","p__Proteobacteria","c__Alphaproteobacteria","o__Sphingomonadales","f__Sphingomonadaceae","g__Sphingomonas","s__Sphingomonas sp."]},{"id":"OTU_11","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Listeria marthii"]},{"id":"OTU_12","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Staphylococcaceae","g__Staphylococcus","s__Bacteria"]},{"id":"OTU_13","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_14","metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Salmonella","s__Salmonella enterica subsp. enterica serovar Agona str. 47.E.09"]},{"id":"OTU_15","metadata":["k__Bacteria","p__Cyanobacteria","c__Melainabacteria","o__Obscuribacterales","f__Bacteria","g__Cyanobacteria","s__Melainabacteria"]},{"id":"OTU_16","metadata":["k__Bacteria","p__Firmicutes","c__Bacilli","o__Bacillales","f__Listeriaceae","g__Listeria","s__Brochothrix sp. 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www/masque/done/file30a47fca2dc3/shaman_silva_annotation.tsv 0 → 100644
View file @ ed1db183
OTU Kingdom Phylum Class Order Family Genus Specie
OTU_13 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Salmonella Salmonella enterica
OTU_49 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp.
OTU_32 Bacteria Firmicutes Bacilli Bacillales Listeriaceae Listeria Listeria marthii