I am interested in detecting methylation regions and I have been using MethylKit.
The method is not very powerful and I want to use more powerful approaches to detect differential methylation.
One way is with HOME (https://github.com/ListerLab/HOME). It mentions using input from BSseeker2.
I would like to know if I can use the bam files generated with bwa-mem, and read-deduplicated and bam-converted with samtools, or if I should do the entire process from the beginning - read trimming/ alignment.
Hi,
I am interested in detecting methylation regions and I have been using MethylKit. The method is not very powerful and I want to use more powerful approaches to detect differential methylation. One way is with HOME (https://github.com/ListerLab/HOME). It mentions using input from BSseeker2. I would like to know if I can use the bam files generated with bwa-mem, and read-deduplicated and bam-converted with samtools, or if I should do the entire process from the beginning - read trimming/ alignment.
Thank you very much;
Juan Pablo