Question: Bowtie Sam Output Not Parsed
gravatar for GPR
7.7 years ago by
GPR320 wrote:

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.

samtools bowtie • 2.6k views
ADD COMMENTlink written 7.7 years ago by GPR320

What organism is this ?

ADD REPLYlink written 7.7 years ago by biorepine1.5k

Human. I have aligned with BWA and Tophat, using different command-lines and succeeding with downstream analyses. Not sure what it wrong with Bowtie.

ADD REPLYlink written 7.7 years ago by GPR320
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