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-   -   Error in Sam to Bam Conversion (http://seqanswers.com/forums/showthread.php?t=27881)

Shishir 02-27-2013 12:43 AM

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!

aggp11 02-27-2013 06:17 AM

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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