Question: Ensembl GTF for Mouse that includes intron, exons, utrs, etc.
1
gravatar for achamess
2.5 years ago by
achamess50
United States
achamess50 wrote:

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.

rna-seq • 1.6k views
ADD COMMENTlink written 2.5 years ago by achamess50

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

ADD REPLYlink written 2.5 years ago by Devon Ryan91k

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

ADD REPLYlink written 2.5 years ago by achamess50

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

BTW, featureCounts is much faster.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Devon Ryan91k

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
ADD REPLYlink written 2.5 years ago by achamess50

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

ADD REPLYlink written 2.5 years ago by Devon Ryan91k
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