Question: Is It Possible To Get Features Count Directly From Tophat?
0
gravatar for samsara
6.2 years ago by
samsara600
The Earth
samsara600 wrote:

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 • 2.9k views
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by samsara600
2
gravatar for Devon Ryan
6.2 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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

ADD COMMENTlink written 6.2 years ago by Devon Ryan94k

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

ADD REPLYlink written 6.2 years ago by Nicolas Rosewick8.7k

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.

ADD REPLYlink written 6.2 years ago by Devon Ryan94k
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