Commit 97494a76 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: new paragraph, "Filtering reads"

parent cdb49924
......@@ -454,6 +454,20 @@ Some datasets may give reads with many low =UNSEG too few= reads:
See [[http://git.vidjil.org/blob/master/doc/browser.org][browser.org]] for information on the biological or sequencing causes that can lead to few segmented reads.
** Filtering reads
It is possible to extract all segmented or unsegmented reads, possibly to give them to other software.
Runing Vidjil with =-U= gives a file =out/basename.unsegmented.vdj.fa=, with all segmented reads.
On datasets generated with rather specific V(D)J primers, this is generally not recommended, as it may generate a large file.
However, the =-U= option is very useful for whole RNA-Seq or capture datasets that contain few reads with V(D)J recombinations.
Similarly, two options are available to get the unsegmented reads:
- =-u= gives a file =out/basename.segmented.vdj.fa=, with unsegmented reads.
- =-uu= gives a set of files =out/basename.UNSEG_*=, with unsegmented reads gathered by unsegmentation cause
Again, as these options may generate large files, they are generally not recommended.
However, they are very useful in some situations, especially to understand why some dataset gives poor segmentation result.
For example =-uu -X 1000= splits the unsegemented reads from the 1000 first reads.
** Segmentation and .vdj format
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