Dear all,

I tried to open a bam file with the following script:

library(Rsamtools)
bam<-scanBam("~/Bamfiles Ivy/W9.1.1.bam")

As a result, a memory error occured:

Error in value[[3L]](cond) : 
  'Realloc' could not re-allocate memory (209715200 bytes)
  file: C:/Users/Diana/Documents/Bamfiles Ivy/W9.1.1.bam
  index: NA

Hence, I am trying to split the file into chunks (chromosomes). The official RSamtools introduction states this code:

> summaryFunction <- function(seqname, bamFile,
+ ...) {
+ param <- ScanBamParam(what = c("pos", "qwidth"),
+ which = GRanges(seqname, IRanges(1, 1e+07)),
4
+ flag = scanBamFlag(isUnmappedQuery = FALSE))
+ x <- scanBam(bamFile, ..., param = param)[[1]]
+ coverage(IRanges(x[["pos"]], width = x[["qwidth"]]))
+ }

However, I don't understand how to fill in the position and qwidth, as I can't read the Bamfile. I tried other things as well, including Seqtools, but it won't work.

I would be VERY grateful if someone could help me out!

I'm not exactly sure what you mean by 'fill in the position and qwidth'. It's possible to find the widths of each chromosome with Rsamtools::scanBamHeader(), and use these to create GRanges corresponding to each seqname (chromosome).

Instead of using scanBam(), use the GenomicAlignments package, readGAlignments() or readGAlignmentPairs() and a ScanBamParam().