Question: Which HTSeq mode is suitable for RNAseq data to be used for differential gene expression?
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gravatar for Arindam Ghosh
11 months ago by
Arindam Ghosh160
India
Arindam Ghosh160 wrote:

Which of the three modes -- union, intersection-strict, intersection-nonempty-- is suitable for RNAseq data to be used for differential gene expression?

rna-seq alignment ngs • 354 views
ADD COMMENTlink modified 11 months ago by h.mon24k • written 11 months ago by Arindam Ghosh160
1

There is no "more suitable" one, all of them will do depending on what you want to achieve! I usually use union but you should check, biologically speaking, which one fits more your system.

ADD REPLYlink written 11 months ago by Macspider2.8k

Go with default, but I would suggest to use FeatureCounts instead of HTSeq. or Salmon.

ADD REPLYlink written 11 months ago by geek_y9.4k

Why? Any explanation for not prefering HTSeq.

ADD REPLYlink written 11 months ago by Arindam Ghosh160
1

featureCounts is:

  1. Much faster (multi-threaded).
  2. No need to sort BAM files but can take sorted ones saving time.
  3. Will create a matrix of reads counts if you feed it multiple BAM files that can be directly used for DE.
ADD REPLYlink modified 11 months ago • written 11 months ago by genomax65k

Also better at assigning PE reads compared to HTSeq.

ADD REPLYlink written 11 months ago by geek_y9.4k

Any room for the pseudo-aligners here, i.e., to avoid the necessity to produce a BAM in the first place? - Kallisto, Salmon, et al.

ADD REPLYlink written 11 months ago by Kevin Blighe41k

If you use STAR as mapper, you can specify the option --quantMode GeneCounts and STAR will output read counts equivalent to htseq --union option. Thus you can skip counting step in your pipeline and save time.

ADD REPLYlink written 11 months ago by grant.hovhannisyan1.5k
0
gravatar for h.mon
11 months ago by
h.mon24k
Brazil
h.mon24k wrote:

As stated above, featureCounts is faster and probably equivalent or better than HTSeq. But to answer directly your question, I will quote the author of HTSeq:

I haven't used anything else than "union" since long, and, admittedly, I would find it hard to now come up with good examples where the intersection modes would be preferable in practice. (When I wrote htseq-count two years ago, that was not so clear yet, of course.)

ADD COMMENTlink written 11 months ago by h.mon24k
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