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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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Workflow question #60

Closed gevro closed 1 month ago

gevro commented 10 months ago

Hi, What is the recommended workflow for generating the required BAM files?

Also, what is the recommended tools for clustering wgbs samples? ie, samples from different tissues and then unbiased clustering to see which samples are similar.

Thank you!

gevro commented 9 months ago

Hello, I am curious if you have advice about this? Thanks!

yonniejon commented 1 month ago

Hi, for generating bam files from fasta files you should use an alignment tool like bwa-meth or bismark on a fasta file. For clustering there is not best option, but hierarchical clustering works well.