advice on data analysis

[riyabelani]

Hello!

I have used this program to extract the DNA methylation levels from data and have bam outputs. I am trying to analyze where methylation is occurring on the genome, but the annotations of the published genome are either not compatible with the Bismark outputs, or there aren't annotations. I used the published reference genome when I used the Bismark program, and the program ran fine. Any advice?

[FelixKrueger]

Bismark does not require, or in fact use, any genome annotations to run. Generally, you need to ensure that both the genome sequence as well as the annotations come from the same source, e.g. all from Ensembl, or all from NCBI, as there are some differences in naming conventions despite using the same underlying sequences. But yea, this is really a separate issue and shouldn't have anything to do with Bismark or its methylation calls.

If you are new to this field I can highly recommend SeqMonk as a user friendly tools look explore and analyse methylation data. Here is a link to a DNA methylation analysis course to show what it capable of (there should also be plenty of tutorial videos on Youtube to help you get started).