best input file format for SeqMonk

[Hedi86]

hello

i am going to identify Differentially methylated regions (DMRs) using SeqMonk. as you know i can use different file format as my imported data. i used BAM, SAM, SAM sorted, COV files from bismark and CpG context taken from bismark extractor. each time i applied exactly same setting (probe definition, ...). I got around 5 million probes for COV and CpG context file, while i got around 1.2 million probes for BAM, SAM and SAM sorted files, which finally resulted in 256 differently methylated genes for COV and CpG context file and only 37 genes for BAM, SAM and SAM sorted files.

all imported files are originally coming from same sequencing file. any idea why im getting such a big difference in DMRs?

what is the best file format as an imported file in order to looked at the DMR and annotate against reference genome using SeqMonk?

thank you for your help.

[fkrueger]

Hi Heidi86,

I think the answer to your question is fairly simple: Bismark coverage files or the CpG methylation call files contain methylation data (as single-base calls), while SAM, BAM or sorted BAM files are simply an alignment format that as such doesn't have anything to do with methylation. In other words, you cannot use BAM files to identify DMRs, but you could use them to more generally look at read coverage or the like.

Allow me to point you to the methylation analysis course here https://www.bioinformatics.babraham....ing.html#bsseq, where you can find examples and practicals of how to use BAM or coverage files for coverage or methylation analysis. Best, Felix

[Hedi86]

thank you so much for your help, the course is awesome

Thank you again