Commit c6a2b573 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: -u/-uu/-uuu

parent 858b8570
......@@ -534,13 +534,17 @@ Runing Vidjil with =-U= gives a file =out/basename.unsegmented.vdj.fa=, with all
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
Similarly, options are available to get the unsegmented reads:
- =-u= gives a set of files =out/basename.UNSEG_*=, with unsegmented reads gathered by unsegmentation cause.
It outputs only reads sharing significantly sequences with V/J germline genes or with some ambiguity:
it may be interesting to further study RNA-Seq datasets.
- =-uu= gives the same set of files, including *all* unsegmented reads (including =UNSEG too short= and =UNSEG too few V/J=),
and =-uuu= further outputs all these reads in a file =out/basename.segmented.vdj.fa=.
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.
For example =-uu -X 1000= splits the unsegmented reads from the 1000 first reads.
** Segmentation and .vdj format
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