Commit 8d35c293 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/user.org: pre-processes, be more explicit for read merging

parent f5e35dfb
......@@ -200,16 +200,17 @@ sense). However please note that the correspondig patients and runs must have
been created beforehand.
**** Pre-processing
The sample files may be preprocessed and this preprocess is chosen when adding
samples. At the moment the only preprocess avalaible is the paired-end read
merging.
The sample files may be preprocessed, by selecting a /pre-process scenario/ when adding a sample.
At the moment the only preprocess avalaible on the public http://app.vidjil.org/ server are the paired-end read merging.
***** Read merging
People using Illumina sequencers may sequence paired-end R1/R2 fragments. It is
*highly* recommended to merge those reads in order to have a read that consists
of the whole DNA fragment instead of split fragments.
To merge R1/R2 fragments, select an adapted /pre-process scenario/ add provide both R1/R2 files as once when adding a sample.
There are two configurations to merge reads. Indeed in case the merging is not
There are two scenarios to merge reads. Indeed in case the merging is not
possible for some reads we must keep one of the fragments (either R1 or
R2). We cannot keep both because it would bias the quantification (as there
would be two unmerged reads instead of one). Depending on the sequencing
......
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