get the intergene region mapped rna-seq read

[jiexiong]

Hi，everyone

I have now worked on my rna-seq data, and mapped the paired-end reads to the reference genome. For detected a background mapped reads, i want to get the reads number for each intergene regions. I have write a perl scripts, but it is very slow. Is there any software to get the mapped for a region in a GFF3 file? (my perl scripts using GFF3 format as input of the intergene region) .

Jie Xiong

[hyjkim]

You can convert the gff3 into a bed file and then use bedTools to report reads intersecting with your annotated intergene regions.