This is a follow up to a question I just posted. I have aligned my reads with Bowtie with the command-line "'bowtie -p 16 -q -n 3 -k 1 -m 1 --best --strata -S BowtieIndex .fastq >& output.sam &" When I try to convert the output SAM file to BAM with "samtools view -bT genome.fa input.sam > output.bam" I get the following error message: " reference 'HWI-ST974:67:C0545ACXX:2:1101:11263:2144' is recognized as ''. Parse error at line 4698: unmatched CIGAR operation" Any help on this? Thanks, G.
Question: Bowtie Sam Output Not Parsed
7.7 years ago by
GPR • 320
GPR • 320 wrote:
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