I am trying to used diffhic to analyze my HiC data. I am getting an error when I use preparePairs:
preparePairs(samplename, hs.Dpn, file=paste(samplename, "h5", sep="."), dedup=TRUE, minq=10)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘seqnames’ for signature ‘"NULL"’
I have made sure that hs.Dpn is a GRanges object with the proper cut sites.
samplename is the name of the bam. I had tried to use the full path to the bam file but that did not work. I created a soft link to the file to avoid the full path but that didnt work. I copied the bam file to the current directory to avoid full paths or soft links but that didnt work either.
I am assuming that the preparePairs method is not able to open the bam file correctly but I am not sure why. Please let me know what I am missing.