Question: Use whole genome bisulfite sequencing to find DNA mutations
0
gravatar for segelmichael
24 months ago by
United Kingdom
segelmichael • 0 wrote:

Hello all, Our lab currently has a large amount of bisulfite sequencing data that a collaborator of mine is looking at. He has methylation sequencing between two conditions. I was wondering whether I could use this same sequencing data to look at genomic variations/mutations (i.e. NHEJ, SNPs, Frame Shift, etc...) between the two samples. I understand how bisulfite sequencing works and what it is used for, but just want to know if there is a tool for this—i.e. something that converts that converted uracils/thymine back into the original cytosine. From there I could proceed from normal!

Thoughts? Thank you all.

Worst comes to worst we will have to repeat with normal WG DNA seq

dna bisulfite sequencing snp • 685 views
ADD COMMENT • link • modified 24 months ago by Devon Ryan • 1.9k • written 24 months ago by segelmichael • 0
1
gravatar for Devon Ryan
24 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

You can do that with BisSNP (note that it's incredibly slow), but as far as I can tell no one has bothered putting it in Galaxy yet (presumably someone could). I should note that bisulfite treatment really lowers the sequencing quality, so don't expect equivalent results to doing WGS at half the depth (half since at Cs you can only use one strand).

ADD COMMENT • link written 24 months ago by Devon Ryan • 1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour