Counting RNA-seq reads mapped to mRNAs (mouse)

Question

[BA20061006]

Hi!

I need to count the number of reads that can be mapped to mouse mRNAs in a RNA-seq dataset. Much appreciated for any suggestions.

[Ankit]

Use featurecounts or htseq-count. It needs a mouse gtf file too. You can download it from gencode or ucsc.

[BA20061006]

I will give them a try. Thanks!

Answer 1

[Ram]

If the reads are from a mixed-organism source, you can use software like BBSplit or Xenome to split reads into species specific files.