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.
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.
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