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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?


aggp11 02-27-2013 06:17 AM


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.

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