In TF ChIP-Seq experiments, ENCODE project provides two types of signal BigWig files: fold change over control and signal p-value. I'm unable to locate the specific pipeline for creating the signal p-value BigWig files. Although MACS2 is mentioned, it appears that the resulting BigWig file is not a peak file but rather a coverage file.
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jomo018
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Pipeline information is here: https://github.com/ENCODE-DCC/chip-seq-pipeline2 https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#
MACS2 is used for peak calling and signal file generation. There is an option to output the signal pileup files (coverage files) that MACS2 generates during peak calling. These outputs are used in another MACS2 function to compare the treatment and control. Below, I have pasted the commands for this module from my use of the pipeline. These might vary a little depending on the pipeline version. Also, the "tagAlign" format is essentially a paired-end BED alignment file that the pipeline generates during earlier steps, which includes a good amount of processing and filtering, including duplicate removal.
macs2 callpeak -t "treatment.tagAlign.gz" -c "control.tagAlign.gz" -f BED -n "filename_prefix" -g mm -p 0.01 --nomodel --shift 0 --extsize 155 --keep-dup all -B --SPMR
macs2 bdgcmp -t "filename_prefix_treat_pileup.bdg" -c "filename_prefix_control_lambda.bdg" --o-prefix "filename_prefix" -m ppois -S 40.35775
macs2 bdgcmp -t "filename_prefix_treat_pileup.bdg" -c "filename_prefix_control_lambda.bdg" --o-prefix "filename_prefix" -m FE
I don't know why exactly, but I assume because they already remove dups with picard. So maybe just to be sure other reads don't get removed for some reason.
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