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