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Blaise LI
bioinfo_utils
Commits
6fcd8adc
Commit
6fcd8adc
authored
Oct 03, 2018
by
Blaise Li
Browse files
DESeq2 and bigwig files for unique mappers.
parent
5946a7a6
Pipeline
#7136
failed with stages
in 46 seconds
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1
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1
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RNA_Seq_Cecere/RNA-seq.snakefile
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6fcd8adc
...
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@@ -371,7 +371,9 @@ if contrasts_dict["ip"]:
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}",
"{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast_type=["ip"],
#counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
counter=COUNTERS, mapped_type=[f"on_{genome}"],
contrast_type=["ip"],
orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["mean_log2_RPM_fold"], id_list=ID_LISTS),]
else:
...
...
@@ -382,7 +384,8 @@ if contrasts_dict["de"]:
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}", "fold_boxplots_{mapped_type}",
"{contrast_type}_{orientation}_{biotype}_{fold_type}_{id_list}_boxplots.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast_type=["de"],
counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast_type=["de"],
orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["log2FoldChange"], id_list=ID_LISTS),]
else:
...
...
@@ -392,16 +395,19 @@ de_files = [
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_counts_and_res.txt"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES),
counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES),
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_{fold_type}_distribution.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
fold_type=["log2FoldChange"]),
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{counter}",
"deseq2_{mapped_type}", "{contrast}", "{orientation}_{biotype}", "{contrast}_MA_with_{id_list}.pdf"),
counter=COUNTERS, mapped_type=[f"on_{genome}"], contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
counter=COUNTERS, mapped_type=[f"on_{genome}", f"unique_on_{genome}"],
contrast=DE_CONTRASTS, orientation=ORIENTATIONS, biotype=DE_BIOTYPES,
id_list=ID_LISTS + ["lfc_statuses"]),
de_fold_boxplots]
...
...
@@ -420,11 +426,13 @@ bigwig_files = [
OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_{rep}",
"{lib}_{rep}_{orientation}_{mapped_type}_by_{norm_type}.bw"),
lib=LIBS, rep=REPS, orientation=ORIENTATIONS,
#mapped_type=[f"on_{genome}", f"unique_on_{genome}"], norm_type=NORM_TYPES),
mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES),
expand(
OPJ(output_dir, aligner, f"mapped_{genome}", "{lib}_mean",
"{lib}_mean_{orientation}_{mapped_type}_by_{norm_type}.bw"),
lib=LIBS, orientation=ORIENTATIONS,
#mapped_type=[f"on_{genome}", f"unique_on_{genome}"], norm_type=NORM_TYPES),]
mapped_type=[f"on_{genome}"], norm_type=NORM_TYPES),]
if spikein_microliter_equivalent:
...
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@@ -610,6 +618,8 @@ def source_sam(wildcards):
##
elif mapped_type == f"polyU_on_{genome}":
return rules.remap_on_genome.output.sam
elif mapped_type == f"unique_on_{genome}":
raise NotImplementedError(f"{mapped_type} only handled from count level on.")
else:
raise NotImplementedError(f"{mapped_type} not handled (yet?)")
...
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