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guoweilong / cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
https://cgmaptools.github.io
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Is cgmaptools supported bwameth bam files ? #71

Open Wong718 opened 1 month ago

Wong718 commented 1 month ago

Hello Weilong. It's a wonderful tool for methylation downstream analysis. Because it takes a long time for Bsseeker2 to align my data, I chose bwameth for mapping and was generating bam files. And I wonder if cgmaptools is compatible with bwameth and what's the different among bam files generated by distinct alignment tools.

guoweilong commented 1 month ago

Thanks. I have not test it with bwameth by myself. Acturally, you can following the suggestions (in Q&A) to speed up BS-Seeker2 for alignment: https://github.com/BSSeeker/BSseeker2#questions--answers

Also, you can also used CGmapTools if you can creat CGmap file from outputs by other aligners.

Best,

Weilong

At 2024-10-10 21:29:25, "William Wong" @.***> wrote:

Hello Weilong. It's a wonderful tool for methylation downstream analysis. Because it takes a long time for Bsseeker2 to align my data, I chose bwameth for mapping and was generating bam files. And I wonder if cgmaptools is compatible with bwameth and what's the different among bam files generated by distinct alignment tools.

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