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