Commit bd7ede21 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/workflow.md: .filtered.fa.gz

following !916
parent 11e96948
Pipeline #215044 passed with stages
in 2 minutes and 18 seconds
......@@ -60,9 +60,9 @@ Starting from `R1.fastq` and `R2.fastq`:
- 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 -g germline/homo-sapiens.g merged-reads.fastq.gz`
- Filter: `vidjil-algo --filter-reads --gz -g germline/homo-sapiens.g merged-reads.fastq.gz`
The resulting `reads-merged.detected.fa` files can be uploaded on any Vidjil server,
The resulting `merged-reads.filtered.fa.gz` file can be uploaded on any Vidjil server,
or re-analyzed with vidjil-algo or with other software.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment