Hello, I have ran Bowtie with the following command-line: 'bowtie -p 16 -q -n 3 -k 1 -m 1 --best --strata -S BowtieIndex *.fastq >& output.sam &' When running CleanSam.jar to remove overhanging reads, I get the following error: "Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields" I do not get this error when I align my reads with BWA or TopHat Any suggestions on how to fix this one? Thanks, G.
Question: Bowtie Output "Not Enough Fields"
7.2 years ago by
GPR • 320
GPR • 320 wrote:
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