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  • Problems with SPP read.bams.tags

    Hi,

    I'm trying to use SPP to analyze chip-seq data. worked fine on a single bam file. Now, I wanted to combine 2 bam files and apply SPP to the merged set.

    This is what I did:

    samtools sort sorted1.bam file1.bam
    samtools sort sorted2.bam file2.bam

    samtools merge merged.bam sorted1.bam sorted2.bam
    samtools index merged.bam

    next in R:
    >library("spp")
    >chip.data=read.bam.tags("merged.bam")
    BGZF ERROR: unable to open file merged.bam
    ERROR: failed to open BAM file 'merged.bam'

    Any ideas, what went wrong?
    loading the initial files (file1, file2) was possible, the sorted ones, however could also not be loaded.

    I checked with ScanBamParam and that was possible, too:

    param <- ScanBamParam(what = what)
    bam <- scanBam("merged.bam", param=param)

    Any comment and help more than wellcome

    Thanks
    Last edited by EdinG; 04-09-2013, 07:14 AM.

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