ChIPQC error <<Unable to process. Each bam file must be associated with at most one peakset.>>
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.
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tsomakiank •
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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.
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.
Do you have only one sample? Adding one more sample might fix your problem.
Yes I only have one sample. I will try adding another one.
Ooooh it finally worked! Thanks a lot Marco!