Dear all,

We have the fly spike-in ChIP-seq data, I use the following tab to calculate the correlation factor,

File/Sample name    DMSO_input  Induced_Input   DMSO_TF1    Induced_TF1
ChIP target         TF1 TF1
Treatment   DMSO    induced DMSO    induced
Tags mapped to entire dm3 genome    82,362  84,401  2,179,901   662,991
Correction factor based on all dm3 alignments       1.024756562     0.304138124

Fly tags(unique)    82,362  84,401  2,179,901   662,991
Human tags(unique)  30,534,368  33,182,250  29,193,791  26,111,001

 Scaled human tags (all dm3 alignments)         32,380,617       85,852,443 
plusDox Global signal relative to Dox  (all dm3)        1.060       2.941

Then I use macs2 bdgopt command to multiply the correlation factor for the treatment and control bdg file,

macs2 bdgopt -i TF1_treat_pileup.bdg -m multiply -p 2.941 -o TF1_treat_norm.bdg
macs2 bdgopt -i TF1_control_lambda.bdg -m multiply -p 1.060 -o TF1_control_norm.bdg

macs2 bdgcmp -t TF1_treat_norm.bdg -c TF1_control_norm.bdg -m ppois -o TF1_dm3_pvalue.bdg
macs2 bdgpeakcall -i TF1_dm3_qvalue.bdg -c 7 -l 186  -o TF1_dm3_peaks_pvalue.bed

I am not sure whether I am right to do peakcalling like this, I just think if I increase the treatment signal 3 times, and the input signal is almost same with before, it will have a lot false peak calling. Can anyone please give me some suggestions how to do the peak calling after the dm3 normalization? Thanks.

HY