Hi,
I'm working with adna and use mapdamge to rescale base qualitys specific to the damage patterns of adna.
Everything works fine for single end reads but with paired end reads I get this errormassage:
Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate
Calls: plot.length ... aggregate -> aggregate.default -> aggregate.data.frame
Execution halted
Error: plotting with R failed
It looks like a problem with R, but that could not be the case because everything works fine for SE, as mentioned above.
The mapdamage homepage says:
"We assume the pairs are facing inwards when counting the position specific misincorporations and rescaling quality scores. An additional assumption in the rescaling process is the pairs are non-overlapping. Make sure the pairing information in the BAM/SAM file is correct as we rely on the paired end information provided by the file"
So i tryed
-samtools view -f 0x02 -b in.bam > out.aligned.bam
-samtools view -h -F 4 -b in.bam > out.bam and
-clipOverlap to edit the bamfiles before I use mapdamage.
nothing helps.
any idea?
I'm working with adna and use mapdamge to rescale base qualitys specific to the damage patterns of adna.
Everything works fine for single end reads but with paired end reads I get this errormassage:
Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate
Calls: plot.length ... aggregate -> aggregate.default -> aggregate.data.frame
Execution halted
Error: plotting with R failed
It looks like a problem with R, but that could not be the case because everything works fine for SE, as mentioned above.
The mapdamage homepage says:
"We assume the pairs are facing inwards when counting the position specific misincorporations and rescaling quality scores. An additional assumption in the rescaling process is the pairs are non-overlapping. Make sure the pairing information in the BAM/SAM file is correct as we rely on the paired end information provided by the file"
So i tryed
-samtools view -f 0x02 -b in.bam > out.aligned.bam
-samtools view -h -F 4 -b in.bam > out.bam and
-clipOverlap to edit the bamfiles before I use mapdamage.
nothing helps.
any idea?
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