not working on Bismark run with bowtie --local

jsh58 / DMRfinder

Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data

MIT License

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not working on Bismark run with bowtie --local #17

Closed JHBI115 closed 5 months ago

JHBI115 commented 1 year ago

Hi,

is there any option to run DMRFinder after running Bismark with bowtie2 --local option ? extract_CpG_data.py crashes because it does not expect CIGAR string to have a "S".

Thank you !

jsh58 commented 1 year ago

Thanks for the question. No, extract_CpG_data.py understands only the CIGAR ops M, D, and I. Soft-clipped alignments are not allowed.

JHBI115 commented 1 year ago

OK, thanks for confirming.