Hi

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

Hi

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

Cheers,

 - Gord