Question: Counting RNA-seq reads mapped to mRNAs (mouse)
0
gravatar for BA20061006
25 days ago by
BA200610060
BA200610060 wrote:

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.

rna-seq • 95 views
ADD COMMENTlink modified 25 days ago by RamRS28k • written 25 days ago by BA200610060

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

ADD REPLYlink written 25 days ago by Ankit140

I will give them a try. Thanks!

ADD REPLYlink written 25 days ago by BA200610060
0
gravatar for RamRS
25 days ago by
RamRS28k
Houston, TX
RamRS28k wrote:

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

ADD COMMENTlink written 25 days ago by RamRS28k
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