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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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running bwameth.py tabulate on Ecoli data #17

Closed avilella closed 6 years ago

avilella commented 9 years ago

Hi,

I am running bwameth.py tabulate on an Ecoli bisulfite treated sample aligned with bismark/bowtie2.

I was getting no methylation calls with the default parameters, so I changed to --context all and ran a parameter sweep on the --map-q option. If I run this on the first 1000bp of the Ecoli genome, I get no calls for mapq values ranging from 60-43, but then I get 138 lines in the meth.vcf file from map-q 42 downwards.

Any ideas what would be a good way of running bwameth/BisSNP on Ecoli data like this?

I read a paper that says Ecoli methylation is found in around 1-2 cases every 1000bp for the CmCWGG motif, but I am unsure how to specify that in BisSNP. Is it possible?

brentp commented 9 years ago

I think it's better to use something like PileOMeth or maybe biscuit if you have trouble with tabulate_methlation since it's just a thin wrapper around BisSNP.