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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
139 stars 53 forks source link

aligning to CTOT+CTOB -- equivalent of bismark --pbat #19

Open avilella opened 8 years ago

avilella commented 8 years ago

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?

brentp commented 8 years ago

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.

Shicheng-Guo commented 7 years ago

Yes. Just get the complement human reference and build G->A index. The problem is how to integrate this function in the main-pipeline.

avilella commented 7 years ago

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 notifications@github.com 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.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/bwa-meth/issues/19#issuecomment-259905407, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJpN_Yl-6xRu3PoA-SceadoFTg-_Dgoks5q9CWvgaJpZM4Fl89h .

Shicheng-Guo commented 7 years ago

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

avilella commented 7 years ago

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 notifications@github.com 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.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/bwa-meth/issues/19#issuecomment-259912315, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJpN3jzf6zmP_4lrzjGyWMoIM2Dn4cBks5q9C8HgaJpZM4Fl89h .