Is It Possible To Get Features Count Directly From Tophat?

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?

tophat2

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written 12.5 years ago by samsara

1 answer

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

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written 12.5 years ago by Devon Ryan

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

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written 12.5 years ago by Nicolas Rosewick

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.

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written 12.5 years ago by Devon Ryan

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