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GreenleafLab / chromVAR

chromatin Variability Across Regions (of the genome!)
https://greenleaflab.github.io/chromVAR/
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Error Running chromVAR - duplicate rownames not allowed #16

Open KASHISH72 opened 7 years ago

KASHISH72 commented 7 years ago

Hi,

I am trying to run chromVAR on ATACseq data and I am providing it a merged bed file from all the peaks and also the bam files. But it is generating a error. Error is: Error in rownames<-(*tmp*, value = c("1", "1", "1")) : duplicate rownames not allowed

But the names are not duplicate and I have also added rgtag using picard tools. Can you tell me what kind of peaks file it require as I have three samples and I have used bedtools merge bed to merge the bed file into one.

Thanks, Kashish

AliciaSchep commented 7 years ago

@KASHISH72 Can you clarify exactly which command is leading to this error?