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Old 01-31-2012, 10:08 AM   #2
Location: Denver, CO

Join Date: Mar 2011
Posts: 37

there may be problems in other areas, but it's difficult to troubleshoot with the given information. things that would help are fragment and read length, whether the reads are actually paired-end or not.

for the final problem though, it's likely as simple as it suggests. just sort the output using:
samtools sort aln.bam aln.sorted

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