Commit aeaa27cf authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: -U/-u, typos

parent f786619d
......@@ -593,7 +593,7 @@ See [[http://git.vidjil.org/blob/master/doc/browser.org][browser.org]] for infor
** 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.
Runing Vidjil with =-U= gives a file =out/basename.segmented.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.
......@@ -603,7 +603,7 @@ Similarly, options are available to get the unsegmented reads:
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=.
and =-uuu= further outputs all these reads in a file =out/basename.unsegmented.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.
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