Question: Whole Exome From Whole Genome
3
gravatar for Kasthuri
6.4 years ago by
Kasthuri220
United States
Kasthuri220 wrote:

Is there a way I can extract whole exome portions from the whole genome data using any standard tools? I need the whole exome in the bam format.

Thanks -Kasthuri

exome genome • 2.5k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 6.4 years ago by Kasthuri220
4
gravatar for Steve Lianoglou
6.4 years ago by
Steve Lianoglou4.9k
US
Steve Lianoglou4.9k wrote:

If you define your "exome regions" in BED format, you can use something like intersectBed from bedtools to extract the reads from whole genome BAM file.

ADD COMMENTlink written 6.4 years ago by Steve Lianoglou4.9k
1

One of the example tutorials on the galaxy server is extracting exonic regions only from the human genome.

ADD REPLYlink written 6.4 years ago by Dan Gaston7.0k

That was my thought too, but do you know of a place where such a file can be found for a whole genome, like mouse? We do exon capture only, and I've been using the probe .beds, but they are bigger than exons.

ADD REPLYlink written 6.4 years ago by Swbarnes21.4k

.bed files can typically be created from UCSC using the Table Browser. For mouse, you could use the Table Browser to get the regions for any number of transcript models in .bed format.

ADD REPLYlink written 6.4 years ago by Sean Davis24k

Thank you very much for the inputs!

ADD REPLYlink written 6.4 years ago by Kasthuri220
0
gravatar for Malachi Griffith
6.4 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith16k wrote:

Another option is the tool: RefCov

ADD COMMENTlink modified 4.7 years ago by Chris Miller19k • written 6.4 years ago by Malachi Griffith16k
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