Hello!



I am working with cat RNA Seq data and after mapping I wanted to get the
count tables. So, I tried to do it using countOverlaps and
summarizedOverlaps in R and HTSeq in python. I've noticed that using R, per
one sorted .bam file (~20*10^6 reads), no matter which previously mentioned
method I used, it takes ~20 hours. In python, it takes ~15 minutes. For R
methods I used GRangesList object downloaded directly in R from Biomart. In
HTSeq I used GTF file provided on Ensembl homepage. Average  cat gene width
is about 44000 in GRangesList.
Does anyone know why getting count tables in R takes so long compared to
HTSeq?


Thank you!

Best,
Milica

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