Hi all,
It is my first attempt with longread data and I am wondering if it is possible to use the ChromVar getCounts function on a bam file produced by long read sequencing?
I have tried the function:
fragment_counts <- chromVAR::getCounts(bamFile, peak.gr, paired = F, by_rg = FALSE, format = "bam")
and received the following error message
"Error in .new_IRanges_from_start_width(start, width) :
'start' or 'width' cannot contain NAs".
But neither start nor width are NAs in the GRange object containing the peaks, and the chromosome names are similar in the peakfile and the bam.
Does anyone have experience with this type of data?
Hi all,
It is my first attempt with longread data and I am wondering if it is possible to use the ChromVar getCounts function on a bam file produced by long read sequencing?
I have tried the function:
fragment_counts <- chromVAR::getCounts(bamFile, peak.gr, paired = F, by_rg = FALSE, format = "bam")
and received the following error message
"Error in .new_IRanges_from_start_width(start, width) :
'start' or 'width' cannot contain NAs".
But neither start nor width are NAs in the GRange object containing the peaks, and the chromosome names are similar in the peakfile and the bam.
Does anyone have experience with this type of data?