Plotting MBD-seq results
1
0
Entering edit mode
2.3 years ago

Does anyone know of any programs or R packages to plot MBD-seq methylation status results like this? Thanks!

I'm using the R package MEDIPS for my analysis.

enter image description here

methylation mbd-seq • 762 views
ADD COMMENT
4
Entering edit mode
2.3 years ago
cmdcolin ★ 1.5k

The deepTools package can do things like this

https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html

You would prepare coverage files in the form of bigwigs with computeMatrix

https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html\

Converting aligned reads to bigwig is generally done from things like macs, which automatically makes wig files, or bedtools genomecov which creates a bedgraph file from a inputted bam, and then run bedGraphToBigWig

ADD COMMENT
0
Entering edit mode

Very helpful, thanks! I wonder if you'd also know what package to use for performing GO annotations on MEDIPS results? I'd like to do GO annotations so I can visualize the results with clusterProfiler.

ADD REPLY

Login before adding your answer.

Traffic: 2315 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6