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icgc-argo / seq-tools

Command line tools for ARGO sequencing data validation
https://github.com/icgc-argo/seq-tools
GNU Affero General Public License v3.0
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Detect `RNA-seq strandedness` in FASTQ #92

Open edsu7 opened 2 years ago

edsu7 commented 2 years ago

We need to run an alignment on our FASTQ files or a subset of them to determine the strandedness; need to add this check to our quite of seq-tools checks

b-f-chan commented 2 years ago

Suggestion: @edsu7 can you investigate Salmon to see if it can do this instead of us coding this into our scripts

https://salmon.readthedocs.io/en/latest/library_type.html#fragment-library-types

b-f-chan commented 2 years ago

Started this work, but encountered issues, may need to run on Linux not MacOS

edsu7 commented 2 years ago

~Based on below, it should take \~15 minutes for 600 million reads.~

Posted into the wrong ticket. Table removed

b-f-chan commented 2 years ago

Had to pull public data to be used; work ongoing

b-f-chan commented 2 years ago

On hold due to other priorities

b-f-chan commented 1 year ago

Targeting PR for this week

Some separate investigation required for NF-Core support

b-f-chan commented 1 year ago

Still low priority, leaving PR open until testing can be done

puneet-oicr commented 1 year ago

No new updates

puneet-oicr commented 1 year ago

No new updates