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
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