Question

Error with dba.count function

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VCLRAC001 • 0

@vclrac001-14183

Last seen 7.1 years ago

Hi

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
Elle

diffbind dba.count • 1.7k views

ADD COMMENT • link updated 7.1 years ago by Gord Brown ▴ 670 • written 7.1 years ago by VCLRAC001 • 0

score 0 · Answer 1 · 2017-10-16

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Gord Brown ▴ 670

@gord-brown-5664

Last seen 3.9 years ago

United Kingdom

Hi,

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...

Cheers,

- Gord

ADD COMMENT • link 7.1 years ago Gord Brown ▴ 670

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Hi

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 REPLY • link 7.1 years ago VCLRAC001 • 0

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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 REPLY • link 6.6 years ago liz.lamarca • 0