Hello, everyone !
I'm looking for a way to use HTseq with multi-thread.
I couldn't find any options about multi-thread.
Anybody knows how to, please ?
(I know there are tools support multi-thread like STAR, HISAT2. but just wonder whether HTseq doesn't support it.)
Thank you. : )
1 answer
HTSeq-count (I guess that is what you are referring to) doesn`t support it as of now for a single file, see the issue for the discussion and alternatives: https://github.com/htseq/htseq/issues/7#issuecomment-638075405
To be precise (citing the developer)
That's it. The -n can process up to n BAM files in parallel to speed up, but cannot use multiple cores on the same file.
Other HTSeq commands are muti-threaded and support the -n option though.
You could use featureCounts instead if you really need multi-threading support. Or run HTSeq count through parallel on multiple files, but this will not scale favorably complexity-wise (duplicated coordinate parsing, duplicated tree structures, increased simultaneous file IO), so this is not recommended.
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