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02-27-2013, 01:43 AM
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#1 |
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Member
Location: Germany Join Date: Nov 2012
Posts: 22
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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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02-27-2013, 07:17 AM
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#2 |
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Member
Location: Wisconsin Join Date: Jun 2011
Posts: 87
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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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| Tags |
| bamtools, bioinfomatics, perl, rnaseq, samtools |
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