Question: Error with dba.count function
gravatar for VCLRAC001
13 months ago by
VCLRAC0010 wrote:


I am analyzing ATAC-seq data for 12 samples. My sample sheet looks as follows (for the first sample):

Sample ID    Tissue    Replicate    BamReads    Peaks    PeakCaller
Sample1    FL    1.1    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped.bam.sort    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped_macs2_peaks.bed.sort    bed

I made a Correlation Heatmap without any problem, but when trying to do a read count with dba.count it keeps giving me the following error:
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  :
  Can't count: some peaksets are not associated with a .bam file.

I am not sure whether this means that it cannot access my bam files, and if so what the problem would be; as my bed files can be accessed, and they have the same file path.

Thanks for any advice in advance


ADD COMMENTlink modified 13 months ago by Gord Brown580 • written 13 months ago by VCLRAC0010
gravatar for Gord Brown
13 months ago by
Gord Brown580
United Kingdom
Gord Brown580 wrote:


Diffbind is sensitive to filename suffixes.  Bam files must end with ".bam".  In hindsight probably a bad design choice.. seemed like a good idea at the time...


 - Gord

ADD COMMENTlink written 13 months ago by Gord Brown580


I followed your advice and renamed all my samples appropriately. Unfortunately, I still get the exact same error message. Could there be something else I am missing?

- Elle

ADD REPLYlink written 13 months ago by VCLRAC0010

I was having the same problem, then realized instead of "bamReads" I had "bamRead" in my sample sheet.  Very sensitive to syntax, maybe check your headers. (Your "B" is capitalized, maybe it's that?")

ADD REPLYlink modified 6 months ago • written 6 months ago by liz.lamarca0
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