Is It Possible To Get Features Count Directly From Tophat?
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10.5 years ago
samsara ▴ 630

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 • 4.0k views
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10.5 years ago

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

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

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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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