Question: Merged vs. Ensembl GTF for htseq-count
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gravatar for kousi31
5 months ago by
kousi3130
kousi3130 wrote:

I have downloaded genome and gtf files from Ensembl. I have aligned my reads using hisat2. I am planning to get raw read counts using htseq count to use in deseq2. Many pipelines have used Ref GTF files for htseq count. I have a doubt as whether I should create a merged gtf file using stringtie or use ensembl gtf? Your suggestions will be helpful.

rna-seq htseq-count • 177 views
ADD COMMENTlink modified 5 months ago by kristoffer.vittingseerup3.4k • written 5 months ago by kousi3130
2
gravatar for i.sudbery
5 months ago by
i.sudbery9.4k
Sheffield, UK
i.sudbery9.4k wrote:

If you are working in a well annotated species (which seems likely if you are getting the GTF from Ensembl), then using the Ensembl annotation is almost certainly sufficient. This is particularly true if you are going to use gene level counts via htseq count - at best StringTie will detect some new isoforms of existing genes (which may or may not be correct), but likely that will be new combinations of existing exons, and since htseq doesn't distinguish between isoforms anyway, the gene level count will be the same.

ADD COMMENTlink written 5 months ago by i.sudbery9.4k
1
gravatar for kristoffer.vittingseerup
5 months ago by
European Union
kristoffer.vittingseerup3.4k wrote:

I've written a bit about such considerations here - hope this is helpfull.

ADD COMMENTlink written 5 months ago by kristoffer.vittingseerup3.4k
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