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Hi All! Hopefully someone can help me here, I'm trying to quantify expression from bowtie2 output.
When I try to used RSEM/eXpress, it fails because it detects that there is something in the header twice e.g. from eXpress
ERROR: Target 'RUMOBE_01512' appears multiple times in BAM header.
RSEM gives pretty much the same thing. Cufflinks however fails because
"Error: sort order of reads in BAMs must be the same" although I suspect it's because of the same thing that's causing the other 2 guys to mess up.
I didn't build the reference used for mapping, but I know it's made of non redundant nucleotide sequences from multiple different bacteria, and the actual alignment was done with bowtie2. So what I'm putting into eXpress/RSEM/cufflinks is a bam file that has been sorted and I've run rmdup on it.
Any idea on how to fix this without going back to the reference and re-aligning?
Thanks
When I try to used RSEM/eXpress, it fails because it detects that there is something in the header twice e.g. from eXpress
ERROR: Target 'RUMOBE_01512' appears multiple times in BAM header.
RSEM gives pretty much the same thing. Cufflinks however fails because
"Error: sort order of reads in BAMs must be the same" although I suspect it's because of the same thing that's causing the other 2 guys to mess up.
I didn't build the reference used for mapping, but I know it's made of non redundant nucleotide sequences from multiple different bacteria, and the actual alignment was done with bowtie2. So what I'm putting into eXpress/RSEM/cufflinks is a bam file that has been sorted and I've run rmdup on it.
Any idea on how to fix this without going back to the reference and re-aligning?
Thanks