Currently I still use htseq-count to perform gene-level quantification (and RSEM for transcript-level by the way), but I found htseq-count being overly cumbersome to use, requiring re-sorting alignments and even the script per se takes extremely long to run.
Right now I'm considering faster alternatives such as Kallisto or Salmon. So what are your experience
Thanks for your input in advance!
Right now I'm considering faster alternatives such as Kallisto or Salmon. So what are your experience
- using it for gene-level differential expression analyses such as edgeR or deSeq2? I understand these programs generate transcript-level output, but they can easily be aggregated. I also wonder how STAR's gene-count output file (ReadsPerGene.out.tab) compare to these.
- For Salmon users: I'd still have to generate an alignment anyway for sequence analyses. Have you noticed any difference between quasi-mapping and alignment-based modes?
Thanks for your input in advance!
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