Hi,
I've successfully ran the test data on my computer and now wanted to run epiAnuefinder on scATAC data from mice. I have my fragment.tsv file generated by 10x cellranger-atac count and have removed any lines with #. I then downloaded the mm10 blacklist file and the mm10 BS genome.
Below is my code:
epiAneufinder(input="mm10fragments_filtered.tsv", #Enter path to your fragments.tsv file or the folder containing bam files
outdir="epiAneufinder_results_Mouse", #Path to the directory where results should be written
blacklist="mm10-blacklist.v2.bed", #Path to bed file that contains the blacklisted regions of your genome
windowSize=1e8,
genome="BSgenome.Mmusculus.UCSC.mm10", #Substitute with relevant BSgenome
exclude=c('chrX','chrY','chrM'), #Exclude for now
reuse.existing=TRUE,
title_karyo="Karyogram of Mouse data",
ncores=1, #'mc.cores' > 1 is not supported on Windows
minFrags=20000)
But then I get the following error:
Subtracting Blacklist...
Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
attempt to set too many names (1) on IRanges object of length 0
Do you know what could be causing this? Is one of my files incorrect?
Hi, I've successfully ran the test data on my computer and now wanted to run epiAnuefinder on scATAC data from mice. I have my fragment.tsv file generated by 10x cellranger-atac count and have removed any lines with #. I then downloaded the mm10 blacklist file and the mm10 BS genome.
Below is my code: epiAneufinder(input="mm10fragments_filtered.tsv", #Enter path to your fragments.tsv file or the folder containing bam files outdir="epiAneufinder_results_Mouse", #Path to the directory where results should be written blacklist="mm10-blacklist.v2.bed", #Path to bed file that contains the blacklisted regions of your genome windowSize=1e8, genome="BSgenome.Mmusculus.UCSC.mm10", #Substitute with relevant BSgenome exclude=c('chrX','chrY','chrM'), #Exclude for now reuse.existing=TRUE, title_karyo="Karyogram of Mouse data", ncores=1, #'mc.cores' > 1 is not supported on Windows minFrags=20000)
But then I get the following error:
Subtracting Blacklist... Error in S4Vectors:::normarg_names(value, class(x), length(x)) : attempt to set too many names (1) on IRanges object of length 0
Do you know what could be causing this? Is one of my files incorrect?
Thank you! Priscilla Glenn