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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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Feature Request: check for gencode while creating index #366

Closed alexvpickering closed 5 years ago

alexvpickering commented 5 years ago

This came up in #336

When building a gencode-based index with salmon index without the --gencode flag, the index that is generated won't work when subsequently running e.g. salmon alevin. This can be a pain to figure out the mistake (missing --gencode flag).

Perhaps some sort of quick grep of the index file name for 'gencode' or within the file for multiple '|'s (used for gencode field separator but not ensembl) should be done to check if it's gencode followed by a warning/error if the --gencode flag is missing? Another possibility could be to just auto-detect if the index is gencode using the above tests, removing the need for the --gencode flag. Thank you

k3yavi commented 5 years ago

Thanks again @alexvpickering . We have fixed this in the develop branch and it will be part of the salmon from the next release which we plan to release very soon.

rob-p commented 5 years ago

Now (since v0.14.0), the index command will issue a warning if you don't pass --gencode but the fasta being indexed looks to be gencode.