Ensembl GTF for Mouse that includes intron, exons, utrs, etc.
I have some RNA-seq data that i aligned using STAR and the Ensembl GRCm38 genome. So, for counting with Htseq, I was going to use the corresponding ensembl gtf. My data is polyA selected, but there is a lot of unspliced RNA, and so a lot will be intron (it's from nuclei). If I just count exons, I'll miss a lot. I want to do a gene level counting. The ensembl GTF file has transcript and gene. I'm assuming gene means the coordinates comprising (exon + intron), but if I wanted to get just introns, how could I do this? I don't see an ensembl GTF that has this as a feature.
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Try setting
-t transcript, which I expect will result in htseq-count using intronic alignments.Thank you. What then is the feature type 'gene' signifying? Is that just exon?
Do you mean
-tor-i? You could also set-t gene, I presume, and have the same result.BTW, featureCounts is much faster.
Here is what I did:
My expectation is that that'll do what you want.