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Old 01-17-2011, 09:35 PM   #1
Junior Member
Location: Japan

Join Date: Jan 2011
Posts: 3
Default Error in samtools merge; different target sequence name

I am now making a script with bowtie and samtools, and
troubled in merging bam files from bowtie.
1) bowtie with every chromosome ewbt; output is sam file
2) sam to bam (every chromosome sam file)
3)* merge all bams
4) bam sort
5) bam index

date=`date +"%Y%m%d_%H%M"`
samtools merge ${date}.bam ${date}_bam_chr1.bam, ${date}_bam_chr2.bam,... ,${date}_bam_chrY.bam

error massage was
[bam_merge_core] different target sequence name : 'chr1' != 'chr2' in file 20110115_0050_bam_chr2.bam

In this case, date was 20110115_0050.
What was wrong??
Fumumumu is offline   Reply With Quote
Old 01-26-2011, 05:22 AM   #2
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Location: Madrid

Join Date: Sep 2010
Posts: 3


I had the same problem.

Check that chromosomes headers are in the same order in the headers of all the bam files.

jmrosa is offline   Reply With Quote

samtools bowtie

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