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Input

MSPC takes as input a tab-delimited file in BED format for each replicate, each containing enriched regions (aka peaks) called with a permissive p-value threshold. By default, the columns of the BED files should comply the following field order:

ChromStartEndNameValue

The p-value needs to be in -Log10(p-value) format. More columns can be present, but they will not be parsed.

For instance:

chrom   start   end     name    value
chr1    1000    2000    peak_1  11
chr1    3000    4000    peak_2  22
chr1    5000    6000    peak_3  33
info

  • If your files are not in this format, you may configure MSPC's parser according to your files.

  • If you files are stranded, you would need to adjust the parser accordingly, otherwise, MSPC will read them un-stranded.