if(input$PairedOrNot=='y')HowTo='<h6><strong>Make sur that you click the « Load » button. <br /> Change the working directory and/or verify the pairs matching.</strong></h6>'
if(input$PairedOrNot=='n')HowTo='<h6><strong>Make sur that you click the « Load » button. <br /> Change the working directory.</strong></h6>'
<p>The aim of this part is to provide an easy cluster interface to perform <b>targeted metagenomic analysis</b>. This analysis will be done using the MASQUE pipeline which allows :</p>
<ul>
<li>to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.</li>
<li>to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.</li>
<li>to perform an "uptodate" analysis considering the scientific litterature.</li>
</ul>
<hr></hr>
<h2>Process</h2>
<p>We follow the recommandation described by Robert C. Edgar in <a href="http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2604.html" target="_blank" >Uparse</a> supplementary paper.<br>
The clustering process in MASQUE is performed as the following :<br>
1. Read quality control<br>
2. Dereplication<br>
3. Chimera filtering<br>
4. Clustering<br>
5. Realignment/mapping<br>
6. Taxonomical annotation of the OTU<br>
7. Quality check of every step </p>
<p>You can find more information in the presentation <a href="/aghozlane/masque/blob/master/tp/Targeted_metagenomics.pdf">here</a>. We try to describe the idea behind each step and a complete TP to do it on your own.</p>'
)
#
#
# <\ui> to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.
# to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.
# to perform an uptodate analysis considering the scientific litterature."
# <p>The aim of this part is to provide an easy cluster interface to perform <b>targeted metagenomic analysis</b>. This analysis will be done using the MASQUE pipeline which allows :</p>
#
# <ul>
# <li>to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.</li>
# <li>to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.</li>
# <li>to perform an "uptodate" analysis considering the scientific litterature.</li>
# </ul>
#
# <hr></hr>
# <h2>Process</h2>
#
# <p>We follow the recommandation described by Robert C. Edgar in <a href="http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2604.html" target="_blank" >Uparse</a> supplementary paper.<br>
# The clustering process in MASQUE is performed as the following :<br>
# 1. Read quality control<br>
# 2. Dereplication<br>
# 3. Chimera filtering<br>
# 4. Clustering<br>
# 5. Realignment/mapping<br>
# 6. Taxonomical annotation of the OTU<br>
# 7. Quality check of every step </p>
#
# <p>You can find more information in the presentation <a href="/aghozlane/masque/blob/master/tp/Targeted_metagenomics.pdf">here</a>. We try to describe the idea behind each step and a complete TP to do it on your own.</p>'
# )
# #
# #
# # <\ui> to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.
# # to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.
# # to perform an uptodate analysis considering the scientific litterature."