View Single Post
Old 01-31-2012, 10:08 AM   #2
jbrwn
Member
 
Location: Denver, CO

Join Date: Mar 2011
Posts: 37
Default

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

see: http://samtools.sourceforge.net/samtools.shtml
jbrwn is offline   Reply With Quote