Biostar Beta. Not for public use.
how to extract only exon from copynumber called by Varscan2?
0
Entering edit mode
16 months ago
9521ljh • 10

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??

enter image description here

ADD COMMENTlink
2
Entering edit mode

Can you show us some results/ illustrations ?

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
2
Entering edit mode

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1