Htseq-count Feature type

I am using Htseq-count. I was using the feature= gene. Is it possible to run it using several features simultaneously? feature: genes miRNA, and ncRNA for example? Thanks

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Hi - Only one Feature type value can be entered per job run.

You could modify your GTF dataset to consolidate feature annotation under a distinct, custom “feature” (3rd column) and test how that works out. Note that the requirement that each feature line contains the ID Attribute would still apply.

A GTF dataset is a type of tabular data and tools like these could be used to replace values:

  • Replace Text in a specific column (one value replacement per run)
  • Replace column by values which are defined in a convert file (batch value replacement)

Hi, my question is related to this thread also.
I am trying to use HTseq to count reads on RNAseq data mapped to a mouse genome.
I am getting Ensembl transcript counts, and I can’t figure out how to get ensembl genes instead.