Question: how to extract only exon from copynumber called by Varscan2?
0
gravatar for 9521ljh
5 weeks ago by
9521ljh10
9521ljh10 wrote:

Hi. i have tumor, normal data(DNAsequence)

i run the copy number calling by Varscan2. And then run CBS(DNAcopy of Rpacakge).

but there is so many noise on the graph. I think it is caused by all region of dna.

Therefore i want to extract only exon data from copynumber called from Varscan2.

But How??

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ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by 9521ljh10
2

Can you show us some results/ illustrations ?

ADD REPLYlink written 5 weeks ago by Titus850

oh sorry, i post my result of CBS by DNAcopy!

ADD REPLYlink written 5 weeks ago by 9521ljh10
2

How many samples did you comprare ? I think you should filter the ratio of CNV with the log parameter if you doesn't. You can extract you data using a bed of exome and bedtools (https://bedtools.readthedocs.io/en/latest/)

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Titus850
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