Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
0
0
Entering edit mode
@ee851898
Last seen 9 months ago
Germany

Hello,

I have some ATAC-seq data and I did peak calling with MACS2. Now I want to extract a matrix with raw counts for the called peaks.

My sample sheet looks like this:

SampleID Condition bamReads Peaks PeakCaller mut1 mut ATAC_peaks/mapped/mut1.bam ATAC_peaks/peaks/mut1_peaks.xls macs mut2 mut ATAC_peaks/mapped/mut2.bam ATAC_peaks/peaks/mut2_peaks.xls macs wt1 wt ATAC_peaks/mapped/wt1.bam ATAC_peaks/peaks/wt1_peaks.xls macs wt2 wt ATAC_peaks/mapped/wt2.bam ATAC_peaks/peaks/wt2_peaks.xls macs

The data comes from different samples with different conditions, but sadly it is not possible to have replicates. I know it is not ideal.

Now I try to create a DBA object and then extract the raw counts as follows:

samples <- read.xlsx("ATAC_peaks/metadata_atac.xlsx")
peaks  <- dba(sampleSheet=samples)
black <- dba.blacklist(peaks, blacklist=TRUE, greylist=FALSE)

rawcounts <- dba.count(black, peaks=NULL, score=DBA_SCORE_READS)

counts <- dba.peakset(rawcounts , bRetrieve=TRUE, writeFile = "ATAC_counts.csv")

However when I get to dba.count(black, peaks=NULL, score=DBA_SCORE_READS), I get the following error:

Error in dba.count(black, peaks = NULL, score = DBA_SCORE_READS) : 
  DBA object must contain only counts

However, I have no problem when running the same code without peaks=NULL, score=DBA_SCORE_READS

I am using R version 4.3.1 and DiffBind 3.10.1.

Help is very much appreciated.

DiffBind ATACSeq • 558 views
ADD COMMENT
0
Entering edit mode

I am sorry, I see here that my sample sheet is not readable. I donĀ“t know how to insert tables here. But the first line would be like this:

SampleID Condition bamReads Peaks PeakCaller

mut1 mut ATAC_peaks/mapped/mut1.bam ATAC_peaks/peaks/mut1_peaks.xls macs

ADD REPLY

Login before adding your answer.

Traffic: 589 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6