Hallo everybody,
I am running a bowtie assembly for drosophila.
After the bowtie is finished I'm piping the unmapped reads to tophat to see if I can map some more reads onto the same reference genome.
The sam out from bowtie I than convert into bam and tophat make automatically a bam file
After finishing both runs, I would like to combine both bam files with the samtools merge command:
but I'm keep getting this error message:
I don't exactly understand what this error means.
I used for both runs the same reference genome. in both there are the chromosomes "2L' and 'YHet'.
YHet is the heterochromatin part of the Y chromosome. It comes 4 times in the sorted bowtie bam file but over 4500 times in the sorted tophat bam file.
'2L' reads I have many millions in both files.
why does it has this problem? Is it because I don't have a header in my tophat output file with the chromosomes (@SQ)?
can I set tophat to have an header in the sam or bam files?
Thanks for ant advice,
Assa
I am running a bowtie assembly for drosophila.
After the bowtie is finished I'm piping the unmapped reads to tophat to see if I can map some more reads onto the same reference genome.
The sam out from bowtie I than convert into bam and tophat make automatically a bam file
After finishing both runs, I would like to combine both bam files with the samtools merge command:
Code:
samtools merge -h dilptotal.sam dilptotal_2.bam dilptotal_bowtie.bam dilp_tophat.bam
Code:
[bam_merge_core] different target sequence name: 'YHet' != '2L' in file 'dilp_tophat.bam'
I used for both runs the same reference genome. in both there are the chromosomes "2L' and 'YHet'.
YHet is the heterochromatin part of the Y chromosome. It comes 4 times in the sorted bowtie bam file but over 4500 times in the sorted tophat bam file.
'2L' reads I have many millions in both files.
why does it has this problem? Is it because I don't have a header in my tophat output file with the chromosomes (@SQ)?
can I set tophat to have an header in the sam or bam files?
Thanks for ant advice,
Assa
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