Search
Question: Error with dba.count function
0
gravatar for VCLRAC001
3 months ago by
VCLRAC0010
VCLRAC0010 wrote:

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

 

ADD COMMENTlink modified 3 months ago by Gord Brown560 • written 3 months ago by VCLRAC0010
0
gravatar for Gord Brown
3 months ago by
Gord Brown560
United Kingdom
Gord Brown560 wrote:

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 COMMENTlink written 3 months ago by Gord Brown560

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 REPLYlink written 3 months ago by VCLRAC0010
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 297 users visited in the last hour