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mdshw5 / fastqp

Simple FASTQ quality assessment using Python

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

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Summarize methylation statistics from bisulfite DNA-seq libraries

mdshw5 opened this issue · comments

commented

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:

  • Cycle-specific CpG cytosine methylation
  • Cycle-specific cytosine conversion
  • Methyl-C content percent per read
commented

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