Entering edit mode
6.2 years ago
lhaiyan3
▴
80
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