ChIPQC error <<Unable to process. Each bam file must be associated with at most one peakset.>>

Question

[tsomakiank]

Hello! I am trying to get the qc metrics from an experiment but I keep getting this error. My sample sheet is this:

  SampleID Factor                          bamReads  ControlID           bamControl                          Peaks PeakCaller 
1 SRR3624779  H3K27 .//reads//filtered_SRR3624779.bam SRR3624791 .//reads/filtered_SRR3624791.bam .//peaks//SRR3624779_peaks.bed        bed

I keep getting this error when I am trying to create the chipqc object.

SRR3624779  H3K27   NA bed
Error in ChIPQC(".//samplesheet.csv", annotation = "mm10", chromosomes = "chr1") : 
  Unable to process. Each bam file must be associated with at most one peakset.

[Marco Pannone]

Try adding the full path to your files in the samples sheet. Also specify the full path to your sample sheet when including it in your R code. Lastly, ensure your peaks file includes peaks and is not empty.

[tsomakiank]

Hey Marco thanks for replying! I tried with the absolute paths but I get the same error. I tried both having the samplesheet as a csv and as a dataframe but I get the same error.

[Marco Pannone]

Do you have only one sample? Adding one more sample might fix your problem.

[tsomakiank]

Yes I only have one sample. I will try adding another one.

[tsomakiank]

Ooooh it finally worked! Thanks a lot Marco!