Tophat2 for size filter

Question

[enterid]

Hi , i am new to bioifnromatic i am working on some RNA seq result , i am using TopHat2 for the alignmnet to the ref genome , i was wondering do Tophat2 get function like size filter , i would like to filter those RNA read below 200nt

Thanks

Answer 1

[Devon Ryan]

tophat2 does not support that and you should not be using it anyway.

Use STAR or hisat2 or bbmap instead as they are modern aligners that will be vastly faster and more accurate than tophat2. There is generally little reason to try to exclude rRNA reads. If you're doing the standard differential expression analysis then just don't count rRNA genes (they probably won't even be in your GTF file).