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Old 02-27-2013, 01:43 AM   #1
Shishir
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Location: Germany

Join Date: Nov 2012
Posts: 22
Default Error in Sam to Bam Conversion

Dear all,

I want to convert Sam file into Bam. I am using command $ samtools view -b -S -o bowtie.glob.bam bowtie.glob.sam
but getting error
Parse error at line 25645: invalid CIGAR character
Could someone please help me to solve this problem?

Thanks!
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Old 02-27-2013, 07:17 AM   #2
aggp11
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Location: Wisconsin

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Default

Hi,

Did you make sure that bowtie gave you a sam file as output? In case it didn't check the following post and this might be useful.

http://seqanswers.com/forums/showthread.php?t=8974
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