Anitha Sundararajan | 13 Sep 20:01 2013

Re: error with dba.counts

Hi

I have been trying to use DiffBind to analyze our Chip-seq data and have 
been running into some errors repeatedly.

I first created a samplesheet.csv describing my samples and it looks 
like this:

SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,PeakCaller
meio.1,meiocytes,H3K4me3,N,1,M_meiocytes_H3K4me3.bam,InM_input_meiocytes.bam,meio.vs.in.rep1.def_peaks.bed,MACS
seed.1,seedlings,H3K4me3,N,1,S_seedling_H3K4me3.bam,InS_input_seedling.bam,seed.vs.in.rep1.def_peaks.bed,MACS

I only have two samples (and their respective inputs) with one rep each 
and the peaks were called using MACS v2. The peak caller generated .bed 
files which was used in DiffBind.

I defined the working directory in R first.

I then read the sample sheet in :
 > H3K4.B73=dba(sampleSheet='samplesheet2.csv',peakFormat='bed')

 >H3K4.B73

2 Samples, 38870 sites in matrix (45304 total):
       ID    Tissue  Factor Condition Replicate Peak.caller Intervals
1 meio.1 meiocytes H3K4me3        N         1        MACS     44124
2 seed.1 seedlings H3K4me3         N         1        MACS     41596

generated a plot,
 > plot(H3K4.B73)

And then when I tried to perform dba.counts, it continuously fails on 
me.  I went through the thread to find similar posts and could not find 
a solution.  I tried the floowing command:

 > H3K4.B73=dba.count(H3K4.B73, minOverlap=3)
and this,
 > H3K4.B73=dba.count(H3K4.B73, minOverlap=3, bLowMem=TRUE)
 > H3K4.B73=dba.count(H3K4.B73, minOverlap=3, bLowMem=FALSE)
And they all failed.

Please let me know if you have any insights on it.

Thanks so much for your help in advance.

Anitha Sundararajan Ph.D.
Research Scientist
National Center for Genome Resources
Santa Fe, NM 87505

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