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Old 03-05-2012, 08:42 PM   #1
mediator
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Location: New England

Join Date: Nov 2010
Posts: 27
Default samtools sort bam file error: generate non-existent file

Hi,
The following is the shell script I wrote to use samtools for sorting bam files. The bam files are from pair end Tophat alignment.

Quote:
#!/bin/sh
samtools sort /data/N1.bam /data/N1_sorted
.
.
.
.
The script seemed run OK. But when I do ls -l under the output directory, all the sorted file has a ? inside its file name, like N1_sorted?.bam. Those sorted files are there, except I could not download nor edit them. Any suggestions? Thanks.
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