Filter HT-Seq output for gene subclasses
I was wondering about a straightforward way to filter RNA-seq datasets specifically those coming out of HT-Seq for highly expressed genes in specific subclasses, for instance all TFs (or all sequence specific binding factors) of absolute counts lets say higher than 100? Thanks!
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I'd suggest that you use Ensembl BioMart for this. You could use all genes to get the gene biotype (I think) and join that with your counts to filter on.
Yes I had thought to do this however I don't believe biotype extends to such a subclass, mostly applies to protein_coding vs lncRNA vs miRNA genes etc etc