I've been spending some time researching the advanced options for macs2 and found some inconsistencies that I am not understanding. Specifically, I looked at the Building signal track tutorial ( https://github.com/taoliu/MACS/wiki/Build-Signal-Track ) and saw that the option --SPMR was used prior to bdgcmp. Looking at the bin source code for version 2.1.2, it is stated that
"If you plan to use the signal output in bedGraph to call peaks using bdgcmp and bdgpeakcall, you shouldn't use this option because you will end up with different results. However, this option is recommended for displaying normalized pileup tracks across many datasets."
I understand that SPMR is great for normalizing the treat_pileup.bdg and control_lambda.bdg to visualize directly on a genome browser, but the tutorial seems to be inconsistent with what is written. Is an --SPMR normalization in callpeak truly valid to use before contructing a signal track using bdgcmp? I thought it was initially a new change for version 2.1.2, but the version change log did not show any changes in the options for the version that the tutorial is referring to.
Additionally, if no input controls are available, is the --nolambda option still the way to go (as recommended by the authors in their Jeng et al. 2011 paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120977/).
Thank you! Varun