bwa-meth
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brentp
aligning to CTOT+CTOB -- equivalent of bismark --pbat
I understand that bwa-meth aligns to the c2t converted reference. Would it be possible to change bwa-meth also to align to the g2a converted reference?
I believe this is what bismark calls "--pbat" option.
If not, are there any other tools out there that will wrap up "bwa mem" for bisulfite sequencing that may have this option added?
I don't have the cycles to add this now, but this should be reasonable to add, see the function convert_fasta. I think you'd convert the complement of the reference and the reads as well.
Yes. Just get the complement human reference and build G->A index. The problem is how to integrate this function in the main-pipeline.
As an alternative, I found a solution to this when trying to align data to the other two strands:
The solution is to reverse complement the fastq files, then align to bwa-meth.
I use github.com/lh3/seqtk for the revcom operation,
Hope it helps,
A.
On Fri, Nov 11, 2016 at 8:22 AM, Shicheng Guo [email protected] wrote:
Yes. Just get the complement human reference and build G->A index. The problem is how to integrate this function in the main-pipeline.
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I don't think it is a good way since the uncertainty is too high for this way. I think it is still long way to make bwa-meth popular. I admit that bwa-meth is really faster than other tools
My solution won't work if you have a non-directional sample. Is your data directional?
I agree the limitation remains in the bwa-meth step, but if you sample is directional, you can still make it work...
A.
On Fri, Nov 11, 2016 at 9:01 AM, Shicheng Guo [email protected] wrote:
I don't think it is a good way since the uncertainty is too high for this way. I think it is still long way to make bwa-meth popular.
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