I am currently programming a python script to automate the next generation sequencing process, with some changeable and default parameters along the execution, for super-enhancer calling but I am facing several problems and doubts.
- Is there any way to accelerate/parallelize MACS peak calling process?
- Does it matter for the usage of bedtools, that the inputs are in BED or BAM format? Can I intersect or substract BED with BAM files and vice versa? I read in the documentation that both type of files are accepted as if they were the same but I think I am missing something...
Any comment on these matters would be appreciated! :)
Dan, No need of
-abam? or input file is auto-detected as BAM/BED?
You're right it is -abam file.bam as opposed to just -a. I've edited my answer to reflect that