Commit ae5890aa authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: --grep-reads

Closes #3785.
parent 712253b7
Pipeline #67376 passed with stages
in 32 minutes and 38 seconds
......@@ -452,8 +452,10 @@ This filtering will work as expected when the provided sequence overlaps
With the `--label-filter` option, *only* the windows related to the given sequences are kept.
This allows to quickly filter a set of reads, looking for a known sequence or window,
with the `--out-reads --label-filter --label <sequence>` options:
All the reads with the windows related to the sequence will be extracted to `out/seq/clone.fa-1`.
with the `--grep-reads <sequence>` preset, equivalent to
`--out-reads --label-filter --label <sequence>`:
All the reads with the windows related to the sequence will be extracted
to files such as `out/seq/clone.fa-1`.
## Clone analysis: VDJ assignation and CDR3 detection
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