I know this is an old thread but I would be interested to use this method to get the counts of reads mapping to exons, introns and intergenic regions. I looked up the UCSC link you gave but the site must have changed as I could not get any specific options for introns and exons. Can you, perhaps, suggest an updated version of your method?
Coverage Of Rnaseq: Exonic, Intronic And Intergenic
I would like to determine the % of reads mapping to exons, introns and intergenic regions. I know BEDTools can do this, but I am not sure how to get the GFF files with the information for exons, introns and intergenic regions separately. Any help? Is there a better/easier way?
Thanks!
1 answer
Go to the UCSC table browser here, select your version and knownGene is a good start. Then father down choose BED format and click "get output". The next page will show you options for introns and exons. From there, you can use bedtools complementBed to get intergenic regions.
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