Dear All,

I am using a script to visualize/analyze BAM files which works for all the files that i have....but now I got some published data and the problems start....

So in total here is my script.....

        chr   <- '19' 

        fileName<-c("/data/lena/GG/file_1.bam")

        fragment.size=200
        chr.size<-seqlengths(Mmusculus)[]                 
        which <- GRanges(seqnames=chr,IRanges(1,chr.size))
        what <- c("rname", "strand", "pos", "qwidth","seq","qual")
        param <- ScanBamParam(which = which,what=what)

        chip.bam <- scanBam(fileName, param=param)
        name <- names(chip.bam)
        name


 [1] "19:1-197195432" "19:1-181748087" "19:1-159599783" "19:1-155630120"
 [5] "19:1-152537259" "19:1-149517037" "19:1-152524553" "19:1-131738871"
 [9] "19:1-124076172" "19:1-129993255" "19:1-121843856" "19:1-121257530"
[13] "19:1-120284312" "19:1-125194864" "19:1-103494974" "19:1-98319150"
[17] "19:1-95272651"  "19:1-90772031"  "19:1-61342430"  "19:1-166650296"
[21] "19:1-15902555"  "19:1-16299"     "19:1-1231697"   "19:1-41899"
[25] "19:1-160594"    "19:1-357350"    "19:1-362490"    "19:1-849593"
[29] "19:1-449403"    "19:1-400311"    "19:1-3994"      "19:1-628739"
[33] "19:1-1785075"   "19:1-58682461"  "19:1-5900358"

Normally here for all the other ChIP-seqs I get one value....something like that

chr19:1-61342430

so then I do that

 chip.qual    <-QualityScaledBStringSet(chip.bam[[name]]$seq, chip.bam[[name]]$qual)

 Error in XStringSet("B", x, start = start, end = end, width = width, use.names = use.names) :
 error in evaluating the argument 'x' in selecting a method for function 'XStringSet': Error in chip.bam[[name]] : no such index at level 2

So what am I doing wrong? could you please help me?

Thank you in advance

Best regards Eleni