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Some recent BS-seq programs store methylation information in a SAM tag. One example is [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf). A flag for `--methyl…
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Hi dinhdiep,
I'm very interested in your work and want to conduct methylation haplotype analysis on my bisulfite sequencing data. I am having trouble generating CpG haplotype files using your code.…
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Hello,
I've been using your Revelio with Freebayes to call variants on methylation libraries. We were able to get good agreement between our methylated libraries and benchmarking variant dataset. …
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Hi,
I was wondering if there's a way to allow for specific mismatches when using STAR. For example, can I set my run so it doesn't score a G>A substitution in **any** position?
Thanks!
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Hi,
It is currently stated in the documentation that "Right now we only support the TruSeq Methyl Capture EPIC kit" for the methylation pipeline (https://bcbio-nextgen.readthedocs.io/en/latest/cont…
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Hello!
I was wondering if `methylpy` methylation calling takes care of directional and non-directional libraries? To quote Bismark User guide here
> Bisulfite treatment of DNA and subsequent PCR…
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Hello,
I am trying to run mcall module but segfaulting. I've tried to google/solve it myself, but I haven't had any success.
I am running a target position specific bisulfite sequencing (not WG…
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```
One of the biggest "errors" in bisulfite sequencing is reads that are
completely unconverted. We have investigated this and Yaping has a nice script
to detect them. It's not been a big problem …
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1. Question1: when I use mCaller call 5mC meth but I haven't 5mC model file, do you have 5mC train model to use ? the code like this :
`mCaller.py -m GATC -r reference.fa -e human.0.eventalign.ts…
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