Question: Which HTSeq mode is suitable for RNAseq data to be used for differential gene expression?
0
gravatar for ag1805x
4 months ago by
ag1805x90
India
ag1805x90 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 • 176 views
ADD COMMENTlink modified 4 months ago by h.mon19k • written 4 months ago by ag1805x90
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 4 months ago by Macspider2.5k

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

ADD REPLYlink written 4 months ago by geek_y8.7k

Why? Any explanation for not prefering HTSeq.

ADD REPLYlink written 4 months ago by ag1805x90
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 4 months ago • written 4 months ago by genomax55k

Also better at assigning PE reads compared to HTSeq.

ADD REPLYlink written 4 months ago by geek_y8.7k

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 4 months ago by Kevin Blighe28k

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 4 months ago by grant.hovhannisyan1.1k
0
gravatar for h.mon
4 months ago by
h.mon19k
Brazil
h.mon19k 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 4 months ago by h.mon19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 578 users visited in the last hour