Question: Want read count with respect to geneID instead of transcript IDs
1
gravatar for archana.bioinfo87
24 days ago by
archana.bioinfo87180 wrote:

Hi,

Maybe my question is very basic but I just want to know how I will get the reads count with respect to geneID. I have RNA-seq data and I used htseq-count and got read count in terms of Ensembl Transcript ID.

Thanks

rna-seq forum • 93 views
ADD COMMENTlink modified 24 days ago by lieven.sterck6.4k • written 24 days ago by archana.bioinfo87180
3
gravatar for colin.kern
24 days ago by
colin.kern750
United States
colin.kern750 wrote:

The default arguments for htseq-count will count by Ensembl gene ID. If you got read counts for Ensembl transcript IDs, I'm guessing your command has "-i transcript_id" in it. Remove that. If your GTF file doesn't use the attribute "gene_id" for gene IDs (GTFs downloaded from Ensembl should), you need to specify it with the -i argument, e.g. "-i geneID".

ADD COMMENTlink modified 24 days ago • written 24 days ago by colin.kern750

Thanks. I got the point.

ADD REPLYlink written 24 days ago by archana.bioinfo87180

I have one more query. Now as I have Ensembl gene IDs and I got the gene symbols with each Ensembl gene IDs. Also, I found that some Ensembl gene IDs having the same gene symbol. In this case, if I want read count w.r.t gene symbol then what I have to consider.

Any help is much appriciated.

Thanks

ADD REPLYlink written 24 days ago by archana.bioinfo87180

This might answer your question: Why am I getting different ensembl gene ids for a given gene symbol?

ADD REPLYlink written 24 days ago by colin.kern750
2
gravatar for lieven.sterck
24 days ago by
lieven.sterck6.4k
VIB, Ghent, Belgium
lieven.sterck6.4k wrote:

Have a look in the manual of htseq-count and pay especially attention to the -t and -f parameters. Then look in your GFF file and choose the feature tags that correspond to your question and use those when running htseq-count

ADD COMMENTlink written 24 days ago by lieven.sterck6.4k

Thanks for the help.

ADD REPLYlink written 24 days ago by archana.bioinfo87180
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