How To Tell How Many Reads Aligned To Intron In Tophat2

Question

[dingying85]

Hi All,

I installed tophat2 and cufflink2 and now I want to obtain the reads aligned in the exon regions and reads aligned in the intron regions. Is there a quick way to get these information? Thanks a lot.

Yours, YING

Answer 1

[Mikael Huss]

There are many ways, for example Picard CollectRNASeqMetrics or RSeQC. Or you could use BEDTools on a GTF annotation file, possibly after creating an intron annotation by going through the GTF file and choosing genomic intervals between the exons.

[dingying85]

Thank you so much for the answer!