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.
Use featurecounts or htseq-count. It needs a mouse gtf file too. You can download it from gencode or ucsc.
I will give them a try. Thanks!
If the reads are from a mixed-organism source, you can use software like BBSplit or Xenome to split reads into species specific files.