I am trying to compute count information for each of the peaks/regions in the consensus set. In this step, for each of the consensus regions DiffBind takes the number of aligned reads in the ChIP sample and the input sample, to compute a normalized read count for each sample at every potential binding site.
I use the code: dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE) and my samplesheet is at this link:
However, I get the following error:
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score, :
Some read files could not be accessed. See warnings for details.
In addition: Warning messages:
1: data/alignment_output/10A_1_H3K_aligned.bam not accessible
2: data/alignment_output/10A_2_H3K_aligned.bam not accessible
3: data/alignment_output/10A_1_IgG_aligned.bam not accessible
4: data/alignment_output/10A_2_IgG_aligned.bam not accessible
Please, if someone would be able to help me troubleshoot this, would really appreciate it.