<p>I got RNASeq data in several samples. I checked the FastQC, seems the read quality are good (Hiseq 2000). But the problem is many reads are mapped to intronic region, and the regions have no any reference exons there (Refseq, ensembl, gencode). We don't know what they are. We guess the problem happend in library preparation, the concentration was low. Now the data has come out and we can't re-sequencing, so we want to remove the reads mapped to intronic region, is there a method to do that? Or anyone have an idea about the intronic reads.  Thanks.</p>

<p>If you have a bed file of exonic regions, or gtf, something like that, you can use <a href='https://code.google.com/p/bedtools/'>BEDTools</a> to filter your .bam for reads that fall in the desired coordinates, using intersectBed</p>
