Commit 6f2f5f6e authored by Mikaël Salson's avatar Mikaël Salson
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......@@ -699,11 +699,11 @@ It is possible to extract all reads with or without detected recombinations,
possibly to give them to other software.
- `-U` gives a file `out/basename.detected.vdj.fa` with all reads having a detected V(D)J recombination
- `-u` gives a set of files `out/basename.UNSEG_*`, with not detected reads gathered by 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** not detected reads (including `UNSEG too short` and `UNSEG too few V/J`),
- `-u` gives a set of files `out/basename.UNSEG_*` with reads where /no V(D)J recombination was detected/,
but with nevertheless some significant similarity to some V/J germline genes,
- `-uu` further produce files with all /other/ reads where no V(D)J recombination was detected
(including `UNSEG too short` and `UNSEG too few V/J`),
and `-uuu` further outputs all these reads in a file `out/basename.undetected.vdj.fa`.
As these options may generate large files, they are generally not recommended.
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