How To Tell How Many Reads Aligned To Intron In Tophat2

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

tophat2 rna-seq

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updated 12.8 years ago by Mikael Huss

• written 12.8 years ago by dingying85 •

1 answer

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.

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written 12.8 years ago by Mikael Huss

Thank you so much for the answer!

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written 12.8 years ago by dingying85 •

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