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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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Feature request:: Add support for Bwa-meth output #40

Closed dineshpeace closed 4 years ago

dineshpeace commented 5 years ago

Please add support to process for BWA meth output files

xie186 commented 5 years ago

Hi @dineshpeace: If you use bwa meth, you can use MethyDackel to output the methylation information compatible with ViewBS using the parametter: --cytosine_report

 --cytosine_report  A per-base exhaustive report comparable to that produced
                  with the same option in Bismark's methylation extractor. The
                  output is a tab-separated file with the following columns:
                  chromosome, position (1-based), strand, number of alignments
                  supporting methylation, number of alignments supporting
                  unmethylation, CG/CHG/CHH, trinucleotide context. This is not
                  compatible with --fraction, --counts, --methylKit, or
                  --mergeContext. The produces a single file with a
                  .cytosine_report.txt extension. Note that even bases with no
                  coverage will be included in the output.

Once you get the results, you can follow the ViewBS manual to generate the index file for the report: https://github.com/xie186/ViewBS#preparation-of-input-files-

Please let us know if you have any other information. Thanks.