Commit 3899abfd authored by Vidjil Team's avatar Vidjil Team Committed by Mathieu Giraud

doc/workflow.md: -M 300

discussed together
parent 06d5ef10
Pipeline #217625 passed with stages
in 2 minutes and 36 seconds
......@@ -59,7 +59,7 @@ supposing that R1 reads are "more centered" on the V(D)J junction than R2 reads.
Starting from `R1.fastq` and `R2.fastq` (`flash2` only works with `.fastq` files):
- Merge: `flash2 R1.fastq R2.fastq -m 300 -t 4 -z` (`-t 4` : run on 4 threads)
- Merge: `flash2 R1.fastq R2.fastq -M 300 -t 4 -z` (`-t 4` : run on 4 threads)
- Concatenate the files you want to keep, as for example `cat out.extendedFrags.fastq out.notCombined_1.fastq.gz > merged-reads.fastq.gz`
- Filter: `vidjil-algo --filter-reads --gz -g germline/homo-sapiens.g merged-reads.fastq.gz`
(`germline/` is the path to the gene repertoires directory, in `vidjil-algo-.../`)
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