Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
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@chunhongliu07-14540
Last seen 3.8 years ago

Hello

I am attempting to run differential analysis of my ChIP-Seq data. I have peak output in .xls output from MACS2 that I am trying to input into DiffBind. 

I am using the following code:

dp.K4 <- dba.peakset(NULL,
                    peaks=system.file("2017_K4_peaks.xls", package="DiffBind"),
                    peak.caller="macs", sampID="WT2017",tissue="BM B cells",
                    factor="WT", replicate=1)
dp.K4 <- dba.peakset(dp.K4,
                    peaks=system.file("2036_K4_peaks.xls", package="DiffBind"),   
                    peak.caller="macs", sampID="WT2036",tissue="BM B cells",
                    factor="WT",replicate=2)
dp.K4 <- dba.peakset(dp.K4,
                    peaks=system.file("1945_K4_peaks.xls", package="DiffBind"),     
                    peak.caller="macs", sampID="WT1945",tissue="BM B cells",
                    factor="WT",replicate=3)
dp.K4 <- dba.peakset(dp.K4,
                     peaks=system.file("2016_K4_peaks.xls", package="DiffBind"),
                     peak.caller="macs", sampID="Mutant2016",tissue="BM B cells",
                     factor="Mutant",replicate=1)
dp.K4 <- dba.peakset(dp.K4,
                     peaks=system.file("2035_K4_peaks.xls", package="DiffBind"),   
                     peak.caller="macs", sampID="Mutant2035",tissue="BM B cells",
                     factor="Mutant",replicate=2)
dp.K4 <- dba.peakset(dp.K4,
                     peaks=system.file("1949_K4_peaks.xls", package="DiffBind"),     
                     peak.caller="macs", sampID="Mutant1949",tissue="BM B cells",
                     factor="Mutant",replicate=3)

 

However, when I look at the dba object, I don't see any peaks:

> dp.K4
6 Samples, 0 sites in matrix:
          ID     Tissue Factor Replicate Caller Intervals
1     WT2017 BM B cells     WT         1   macs         0
2     WT2036 BM B cells     WT         2   macs         0
3     WT1945 BM B cells     WT         3   macs         0
4 Mutant2016 BM B cells Mutant         1   macs         0
5 Mutant2035 BM B cells Mutant         2   macs         0
6 Mutant1949 BM B cells Mutant         3   macs         0

My MACS .xls output file has peaks and intervals.

It does not seem to be importing the files correctly.

I am using R 3.4.2 and RStudio 1.1.383

 

I also tried cutting the first 6 columns of the data from the .xls file and importing as a .bed file, but that did not work either.

There were no error messages.

 

Thank you for your help!

 

Cliu

diffbind macs2 chip-seq • 1.3k views
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1
Entering edit mode
@chunhongliu07-14540
Last seen 3.8 years ago

I already figured out and it is because the file path is not correct.

Thanks!

cliu

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