Is It Possible To Get Features Count Directly From Tophat?

Question

[samsara]

I have been using HTSeq to count number of reads per feature for RNA-Seq. I am just wondering, Is it possible to get counts through Tophat by providing GTF file without using HTSeq?

Answer 1

[Devon Ryan]

No, it's not, but you might try featureCounts, which is much faster than htseq-count.

[Nicolas Rosewick]

Did you compare htseq and featureCounts in term of DE genes (using DESeq or edgeR) ?

[Devon Ryan]

No, because the difference in counting is usually very minor. The count differences are almost entirely due to an off-by-one difference in interpretation of GTF/GFF file coordinates.