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


I am analyzing ATAC-seq data for several embryonic replicates. An extract of my sample sheet looks as follows:

Sample ID    Tissue    Replicate    BamReads    Peaks    PeakCaller
Sample1    FL    1.1    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped.bam    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped_macs2_peaks.bed    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 tried a truncated version of my sample sheet, different file paths, and different bam and bed files in various combinations. Every time I get stuck at the same step. Is there anything else I could try?

Thanks for any advice in advance
- L

ADD COMMENTlink modified 11 months ago by Gord Brown570 • written 11 months ago by VCLRAC0010
gravatar for Gord Brown
11 months ago by
Gord Brown570
United Kingdom
Gord Brown570 wrote:


Try changing the column name from "BamReads" to "bamReads".  It's case sensitive, and yes, it's inconsistent with the other column names...


 - Gord

ADD COMMENTlink written 11 months ago by Gord Brown570
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 375 users visited in the last hour