hi, i used to find the difference peak of ATAC-seq by MACS2 bdgdiff, but i cant undersand what the means of the fourth column in results,
the command is macs2 bdgdiff --t1 S5_treat_pileup.bdg \ --c1 S5_control_lambda.bdg \ --t2 S3_NT_treat_pileup.bdg \ --c2 S3_NT_control_lambda.bdg \ --d1 16269407 --d2 11571085 -g 60 -l 120 --outdir S5 --o-prefix S5vs
there are three files after runing this command.
S5vs_c3.0_common.bed S5vs_c3.0_cond1.bed S5vs_c3.0_cond2.bed
S5 sample up-regulated position is stored in the S5vs_c3.0_cond1.bed?
what is the means of the fourth column?
track name="condition 1 (peaks)" description="unique regions in condition 1" visibility=1
chr1 2189806 2189942 S4vs_cond1_1 3.56891
chr1 7586540 7586806 S4vs_cond1_2 16.05824
thank you very much
