I’m trying to call peaks using bdgbroadcall from bdg generates by cmbreps and -m fisher But the out put of the bdgbroadcall contain no p – value or any other than coordinate (below you can find the heading of the output)
track name="peak" description="peak" type=gappedPeak nextItemButton=on
chr1 818930 819140 H3K4me1_H0_1_2_G840.bdg_broadRegion1 0 . 818930 819140 0 2 1,1 0,209 0.00000 0.00000 0.00000
chr1 903599 904278 H3K4me1_H0_1_2_G840.bdg_broadRegion2 0 . 903599 904278 0 3 1,632,1 0,37,678 0.00000 0.00000 0.00000
chr1 905126 907304 H3K4me1_H0_1_2_G840.bdg_broadRegion3 0 . 905126 907304 0 3 1,212,1 0,1915,2177 0.00000 0.00000 0.0000
So this what I did
1 call peaks after removing all duplicates macs2 callpeak -t $INDIR/ Sample1_Mkdup_fliter.bam -c $Input/Input_Mkdup_fliter.bam -f BAM -g hs -n H3K4me1_H0_1 -B --broad -q 0.01 --keep-dup all --nomodel --extsize 210 –outdir
2 compare pileup and lambda for each replicates to get pvalue track macs2 bdgcmp -t rep1_pileup.bdg -c rep1_lambda.bdg -m ppois -o rep1_pvalue.bdg macs2 bdgcmp -t rep2_pileup.bdg -c rep2_lambda.bdg -m ppois -o rep2_pvalue.bdg
3- combine both files macs2 cmbreps -i rep1_pvalue.bdg rep2_pvalue.bdg -m fisher -o rep1_rep2_pvalue.bdg.bdg
4 recall peaks macs2 bdgbroadcall -i rep1_rep2_pvalue.bdg.bdg -c 8 -l 210 -g 76 -o rep1_rep2.bdg
