[BioC] reading BAM files

[Martin Morgan]

Hi Hermann --

On 11/26/2012 09:26 AM, Hermann Norpois wrote:
> Hello,
>
> I try to read BAM files - so far without success. And I dont know why.
>
> My Bamfile is wgEncodeOpenChromDnase8988tAlnRep1.bam
> (downloaded from the Encode site)
>
> For example:
>
> library (ShortRead)

library(Rsamtools)

>> which <- RangesList(seq1=IRanges(1000,2000),
> + seq2=IRanges(c(100,1000), c(1000,2000)))
>> what <- c("rname", "strand", "pos", "qwidth","seq")
>> param <- ScanBamParam(which=which, what=what)
>> bam <- scanBam ("~/Bam/wgEncodeOpenChromDnase8988tAlnRep1.bam",
> param=param)
> [bam_index_load] fail to load BAM index.
> Fehler in open.BamFile(BamFile(file, index), "rb") :
>    failed to load BAM index

index the bam file first

indexBam("~/Bam/wgEncodeOpenChromDnase8988tAlnRep1.bam")

Martin

>    file: /home/hnorpois/Bam/wgEncodeOpenChromDnase8988tAlnRep1.bam
>
>
> The mentioned syntax I copied from an introduction to Rsamtools.
> Actually I would like to know a simple syntax that enables me to read
> BAM-files. Can anybody give me a hint.
>
> Thanks Hermann
>
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>
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