taoliu
commented
7 years ago Control1 and Control2 should be T2D control background and ND background correspondingly. After you run 'callpeaks -B -f BAMPE -t xxx.bam' on T2D and ND ATAC-Seq separately, you would get a '_treat_pileup.bdg' and '_control_lambda.bdg' for each condition. So the setting is: Condition1: T2D_Bcell_treat_pileup.bdg Control1: T2D_Bcell_control_lambda.bdg Condition2: ND_Bcell_treat_pileup.bdg Control2: ND_Bcell_control_lambda.bdg
Hi there,
I'm trying to use MACS2 bdgdiff for my ATAC-seq differential peaks analysis. I want to compare the differential expression between T2D (Type 2 Diabetes) and ND(Non-diabetes, control) with the same cell type. For example, compare T2D_Bcell with ND_Bcell. My question is, in the arguments of bdgdiff, what should I put for the arguments for the analysis? How about: Condition1: T2D_Bcell Control1: ND_Bcell Condition2: ND_Bcell Control2: ND_Bcell ? I want to compare one sample (T2D) with one control (ND). What should I put for condition and control arguments?
Simon