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