Commit 6f62a9f4 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: RNA-Seq/Capture, more documentation

parent 8b92fd45
......@@ -632,6 +632,11 @@ require either the =-G germline/IGH= option, or the multi-germline =-g germline=
# The out/reads.segmented.vdj.fa include all reads where a V(D)J recombination was found
#+END_SRC
Typical whole RNA-Seq or capture datasets may be huge (several GB) but with only a (very) small portion of CDR3s.
Using Vidjil with =-U= will create a =out/reads.segmented.vdj.fa= file
that includes all reads where a V(D)J recombination (or an unexpected recombination, with =-2=) was found.
This file will be relatively small (a few kB or MB) and can be taken again as an input for Vidjil or for other programs.
** Advanced usage
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