Summarize methylation statistics from bisulfite DNA-seq libraries

mdshw5 / fastqp

Simple FASTQ quality assessment using Python

https://pypi.python.org/pypi/fastqp

MIT License

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Summarize methylation statistics from bisulfite DNA-seq libraries #1

Open mdshw5 opened 10 years ago

mdshw5 commented 10 years ago

Some recent BS-seq programs store methylation information in a SAM tag. One example is Bismark. A flag for --methylation would activate routines for summarizing:

[X] Cycle-specific CpG cytosine methylation
[x] Cycle-specific cytosine conversion
[ ] Methyl-C content percent per read

mdshw5 commented 9 years ago

Since there are only a few data formats for representing methylation data from bisulfite sequencing, flags for --bismark, --bsmap etc.. might be useful.