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zyndagj / BSMAPz

Updated and optimized fork of BSMAP
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query regarding methylation level from methylratio output file. #29

Closed CS791 closed 4 years ago

CS791 commented 4 years ago

Hi! Dr. Zynda,

I hope you are doing well.

This is not regarding any issue, it just a query regarding the BSMAPz output file. The file generated from methylratio.py contains 12 columns. I want to plot the methylation level around various genomic features. My question is how I can extract the methylation level from this methylation output file.

I will appreciate it if I get any help regarding this.

Thank you Best regards

Saurabh

zyndagj commented 4 years ago

Hello!

I don't have a standalone solution, but you may be interested in this pipeline.

https://github.com/zyndagj/ZED-bsmap-align

The ZED pipeline aligns reads, calls methylation, and generates summary tracks for post-processing and visualization. If you don't want to re-run your analysis, you may find it helpful as a starting point for a script of your own.

I will add bedgraph output to my development roadmap though.

Sincerely, Greg Zynda