Post peak calling

generate FC signal track

 macs2 bdgcmp -t xxx.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c xxx.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
 --o-prefix xxx.PE2SE.nodup.tn5.pf" -m FE
slopBed -i xxx.PE2SE.nodup.tn5.pf"_FE.bdg -g hg38.chrom.sizes -b 0 | bedClip stdin hg38.chrom.sizes xxx.PE2SE.nodup.tn5.pf.fc.signal.bedgraph
sort -k1,1 -k2,2n xxx.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > xxx.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph
bedGraphToBigWig xxx.pf.fc.signal.srt.bedgraph hg38.chrom.sizes xxx.PE2SE.nodup.tn5.pf.fc.signal.bigwig

• macs2 bdgcmp;
  • Use treat vs. control to calculate fold enrichment
  • -m FE: fold enrichment; or logLR - log likelihood; subtract - subtracting noise from treatment sample
  • -p: adding pseudocount for logLR
• slopBed from BETOOLS can increase the size of each feature file with a user-defined number of bases.
• bedClip: remove lines from bed file that refer to off-chromosome places.
• sort bedgraph and transform to bigwig file

generate pval signal track

macs2 bdgcmp -t xxx_treat_pileup.bdg -c xxx_control_lamda.bdg --o-prefix xxx -m ppois -S ${sval}

• compare pileup and local lambda to get the scores in pvalue -m ppois or qvalue -m qpois
• output track contain th -log10(pval) or -log10(qval) for each basepair through local Poisson test