How to quantify the reads of each peak for ChIP-seq data?

Question

[Dan]

Hello

I can quantify the total reads of all the peaks in a peak file using DiffBind, the tamoxifen.csv:

SampleID    Tissue  Factor  Condition   Treatment   Replicate   bamReads    ControlID   bamControl  Peaks   PeakCaller
BT4741  BT474   ER  Resistant   Full-Media  1   reads/Chr18_BT474_ER_1.bam  BT474c  reads/Chr18_BT474_input.bam peaks/BT474_ER_1.bed.gz bed
BT4742  BT474   ER  Resistant   Full-Media  2   reads/Chr18_BT474_ER_2.bam  BT474c  reads/Chr18_BT474_input.bam peaks/BT474_ER_2.bed.gz bed
MCF71   MCF7    ER  Responsive  Full-Media  1   reads/Chr18_MCF7_ER_1.bam   MCF7c   reads/Chr18_MCF7_input.bam  peaks/MCF7_ER_1.bed.gz  bed
MCF72   MCF7    ER  Responsive  Full-Media  2   reads/Chr18_MCF7_ER_2.bam   MCF7c   reads/Chr18_MCF7_input.bam  peaks/MCF7_ER_2.bed.gz  bed
MCF73   MCF7    ER  Responsive  Full-Media  3   reads/Chr18_MCF7_ER_3.bam   MCF7c   reads/Chr18_MCF7_input.bam  peaks/MCF7_ER_3.bed.gz  bed
T47D1   T47D    ER  Responsive  Full-Media  1   reads/Chr18_T47D_ER_1.bam   T47Dc   reads/Chr18_T47D_input.bam  peaks/T47D_ER_1.bed.gz  bed
T47D2   T47D    ER  Responsive  Full-Media  2   reads/Chr18_T47D_ER_2.bam   T47Dc   reads/Chr18_T47D_input.bam  peaks/T47D_ER_2.bed.gz  bed
MCF7r1  MCF7    ER  Resistant   Full-Media  1   reads/Chr18_TAMR_ER_1.bam   TAMRc   reads/Chr18_TAMR_input.bam  peaks/TAMR_ER_1.bed.gz  bed
MCF7r2  MCF7    ER  Resistant   Full-Media  2   reads/Chr18_TAMR_ER_2.bam   TAMRc   reads/Chr18_TAMR_input.bam  peaks/TAMR_ER_2.bed.gz  bed
ZR751   ZR75    ER  Responsive  Full-Media  1   reads/Chr18_ZR75_ER_1.bam   ZR75c   reads/Chr18_ZR75_input.bam  peaks/ZR75_ER_1.bed.gz  bed
ZR752   ZR75    ER  Responsive  Full-Media  2   reads/Chr18_ZR75_ER_2.bam   ZR75c   reads/Chr18_ZR75_input.bam  peaks/ZR75_ER_2.bed.gz  bed

library(DiffBind)

sample_dir <- "DiffBind_test/"
tamoxifen <- dba(sampleSheet="tamoxifen.csv",
                 dir=system.file("extra", package="DiffBind"))

tamoxifen <- dba.count(tamoxifen)

info <- dba.show(tamoxifen)

info

The output is the total reads of all the peaks in a peak file:

       ID Tissue Factor  Condition  Treatment Replicate Caller Intervals   Reads FRiP
1  BT4741  BT474     ER  Resistant Full-Media         1 counts      2845  652697 0.16
2  BT4742  BT474     ER  Resistant Full-Media         2 counts      2845  663370 0.15
3   MCF71   MCF7     ER Responsive Full-Media         1 counts      2845  346429 0.31
4   MCF72   MCF7     ER Responsive Full-Media         2 counts      2845  368052 0.19
5   MCF73   MCF7     ER Responsive Full-Media         3 counts      2845  466273 0.25
6   T47D1   T47D     ER Responsive Full-Media         1 counts      2845  399879 0.11
7   T47D2   T47D     ER Responsive Full-Media         2 counts      2845 1475415 0.06
8  MCF7r1   MCF7     ER  Resistant Full-Media         1 counts      2845  616630 0.22
9  MCF7r2   MCF7     ER  Resistant Full-Media         2 counts      2845  593224 0.14
10  ZR751   ZR75     ER Responsive Full-Media         1 counts      2845  706836 0.33
11  ZR752   ZR75     ER Responsive Full-Media         2 counts      2845 2575408 0.22

How to quantify the reads of each peak in a peak file for ChIP-seq data? Thanks a lot

Answer 1

[jared.andrews07]

You're probably looking for dba.peakset(tamoxifen).

[Dan]

Yes, dba.peakset(tamoxifen,bRetrieve = TRUE) works. Thanks