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Old 05-22-2015, 02:37 AM   #18
Michael.Ante
Senior Member
 
Location: Vienna

Join Date: Oct 2011
Posts: 123
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Hi Kaps,

try
Code:
samtools view -S 4_S4_paired.sam | head
if you don't get any problems there, proceed with
Code:
 samtools view -bSh 4_S4_paired.sam > 4_S4_paired.bam
The missing '>' was then the problem. If the sam file doesn't have any header lines, you'll need to provide these additionally.

Cheers,

Michael
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