Question: Coverage Of Rnaseq: Exonic, Intronic And Intergenic
1
gravatar for Pfs
8.6 years ago by
Pfs500
United States
Pfs500 wrote:

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!

intron rna coverage • 4.4k views
ADD COMMENTlink modified 8.3 years ago by brentp23k • written 8.6 years ago by Pfs500
4
gravatar for brentp
8.6 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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.

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by brentp23k

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?

ADD REPLYlink written 4.7 years ago by Nick270
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