Ensembl GTF for Mouse that includes intron, exons, utrs, etc.

Question

[achamess]

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.

[Devon Ryan]

Try setting -t transcript, which I expect will result in htseq-count using intronic alignments.

[achamess]

Thank you. What then is the feature type 'gene' signifying? Is that just exon?

[Devon Ryan]

Do you mean -t or -i? You could also set -t gene, I presume, and have the same result.

BTW, featureCounts is much faster.

[achamess]

Here is what I did:

htseq-count --format bam --order pos --mode intersection-strict --type gene --idattr gene_id $ALIGN/STAR- alignments/AC3-Aligned.sorted.bam $REFS/ensembl/Mus_musculus.GRCm38.87.gtf > $RNASEQ/expression/htseq- ensembl/AC3-counts.tsv

[Devon Ryan]

My expectation is that that'll do what you want.