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ijuric / MAPS

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question about run the bash script #37

Open jiangshan529 opened 3 years ago

jiangshan529 commented 3 years ago

Hi, I see there's a need for macs2_filepath. So does it mean I need to first map the fastq files to the reference genome, and then call peaks to get the macs2_narrowpeak_file, and then run the MAPS pipeline again with the fastq files? Thanks!

jiangshan529 commented 3 years ago

can peaks called by other software in bed format as well be used?

armenabnousi commented 3 years ago

MAPS requires ChIP-seq peaks in bed format. If you have ran ChIP experiment, or maybe ATAC-seq you can use the peaks called for those experiments. It does not have to be MACS2 peaks but it's the software generally used for peak calling in ChIP-seq. Just make sure the file is in bed format. I don't think running MACS2 on the reads obtained from PLAC-seq is a good approach.