Q: What is the relationship between the value of the bigwig file generated by macs2 bdgcmp and the read count?

[User-yx]

Hello, the bdg file generated by bdgcmp can convert into a bigwig file, for a particular region, what is the relationship between the signal values I get with bigwig and the reads count I get with the bam file ? bdgcmp -m can be set to ppois or FE etc, what is the difference between them ? Thank you very much!

[taoliu]

The descriptions can be seen after macs2 bdgcmp -h

ppois: the poisson distribution p-value (-log10(pvalue) form) using control as lambda and treatment as observation qpois: q-value through a BH process for poisson pvalues subtract:subtract control from treatment FE: linear scale fold enrichment (treatment/control) logFE: log10 fold enrichment(need to set pseudocount), logLR: log10 likelihood between ChIP-enriched model and open chromatin model/aka control (need to set pseudocount) slogLR: symmetric log10 likelihood between two ChIP-enrichment models max: maximum value between the two tracks. Default option is ppois.