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vidjil
vidjil
Commits
bd7ede21
Commit
bd7ede21
authored
Feb 12, 2021
by
Mathieu Giraud
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doc/workflow.md: .filtered.fa.gz
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@@ -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.
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