How to find out p-value format in chip-seq .bed files from GEO
Hi,
I'm downloading chip-seq peak bed files from GEO and my goal is to combine replicates to a consensus bed file, using MPSC. For example: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207899
The question is, how do i find out if the p-value in the peak bed-file is -log10(p-value) , -10log10(p-value) or -100log10(p-value) ? There is no header row.
Thanks for your help !
1 answer
It says that BED file was generated with MACS. According to the documentation:
The 5th column in this file is the -10*log10pvalue of peak region
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since there are also values between 1000 and 4000 in it, i would have guessed it's -10log10 or -100log10, but it's a pity that there is no other way to say for sure.