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  • Error Bowtie with fastq files (from Solid .csfasta & .qual)

    Hello, I have converted color space .csfasta & .qual to fastq using solid2fastq.pl from maq. When I use the fastq file with bowtie I get this error:
    Reads file contained a pattern with more than 1024 quality values.
    Please truncate reads and quality values and and re-run Bowtie
    terminate called after throwing an instance of 'int'


    I have seen in the forums that this happens when there are uncalled bases with a dot instead of an "N" in the solexa reads. However I do not have dots in my file and I do not have reads as long as 1024 bases.

    When I convert the fastq to fasta an rerun bowtie with the fasta file, it works fine.

    Any suggestions?

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