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
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.