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When is HTSeq Count Script used?

Hello,

I was just wondering when in the pipeline is the HTSeq count function used? Is it only used when DESeq is being used for further analysis? Thanks.

Omar

sequence rna-seq
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written by oma219 • oma219

1 answer

HTSeq can be used for any DE tool that uses raw read counts (hence limma trend, edgeR, DESeq2). You can also try featureCounts instead of HTSeq, which I personally prefer.

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written by Benn Benn

Does feature counts have any additional features over HTSeq? Thanks!

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written by oma219 • oma219

I am not sure, I found it easier in usage...

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written by Benn Benn

1) HTSeq seems to have a bug that causes it to fail with certain libraries: this thread describes a bug that I personally have run into. Note that the thread ran for almost 2 years with no robust fix.

2) featureCounts puts all the results into a single output file, making it slightly easier to load (I don't know if htseq-count supports that, it wasn't obvious to me anyway)

3) featureCounts is faster, according to its authors. See Table 1 in their open access paper. I have also found this, but haven't timed it properly.

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written by gabriel.rosser gabriel.rosser

featureCounts also supports SAM v.1.4 format tags (not to be confused with version of samtools program) and will automatically sort your BAM files as needed. Last time I had looked htseq-count did not do either.

featureCounts is significantly faster than htseq-count as has already been mentioned.

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written by GenoMax GenoMax

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