Question: Seqmonk: Bedgraph as input ? (EPIC methylation array data)
0
gravatar for Ankit
7 weeks ago by
Ankit60
Ankit60 wrote:

Hi everyone,

Is it possible to give Bedgraph of methylation data as input to Seqmonk?

I do not have .cov or .bam. because the data is from EPIC methylation array. I only have Bedgraph.

I uploaded it as text file but it is not giving me strand separated view and rather like a line as in bed file. When I somehow quantitated no difference is observed in methylation pattern, which I clearly observed by UCSC view. I feel something is wrong in the way I am uploading.

I am also not sure how to design probe in seqmonk. I mean the window size, probe size ,step size for such kind of files.

If anyone have a suggestion or previous experience please help!

Thanks

ADD COMMENTlink modified 7 days ago by Charles Warden6.1k • written 7 weeks ago by Ankit60

Any suggestions???? Thanks

ADD REPLYlink written 7 weeks ago by Ankit60

Consider writing to SeqMonk team members directly.

ADD REPLYlink written 7 weeks ago by genomax62k
0
gravatar for Charles Warden
7 days ago by
Charles Warden6.1k
Duarte, CA
Charles Warden6.1k wrote:

I'm not sure why you want to use Seqmonk for analysis of EPIC data.

However, these are some options that you have for EPIC data analysis:

GenomeStudio : pre-processing / beta calculation; some differential methylation

minfi : pre-processing / beta calculation; differential methylation, at either site or region level (with bumphunter)

COHCAP : primarily differential methylation (at site level, then region level)

RnBeads : QC plots; pre-processing and differential methylation

ADD COMMENTlink modified 7 days ago • written 7 days ago by Charles Warden6.1k
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 2.3.0
Traffic: 1679 users visited in the last hour