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  • Bowtie Error Message

    Hello,

    I am trying to map some human reads with Bowtie, and after running the program, I received the message below and did not obtain statistics for mapping. It did apparently map 77.5 million reads with the options added (I did a line count on the output file), but I am not sure if Bowtie finished mapping the reads. The input fastq file came from SRA. I have the most recent version of Bowtie for Linux. Does anyone have any suggestions on how to avoid this error so that Bowtie finishes mapping the reads?

    $ ./bowtie -a -v 2 -m 3 hg19_c -C -q --suppress 1,6,7,8 invitro_1.fastq >invitro_1_mapped.txt

    Saw ASCII character -1 but expected 33-based Phred qual.
    Command: ./bowtie -a -v 2 -m 3 -C -q --suppress 1,6,7,8 hg19_c invitro_1.fastq

    Thanks,
    Clayton

  • #2
    Bowite has many options for different formats of quality score,the default is --phred33-quals,which means the inputs(quality scores) are taken as ASCII characters.
    However,it seems that your RNA-Seq data were SOLiD color space format,and usually SOLiD platforms output quality scores in integer.
    So,try this option "--integer-quals" instead of the default one,I think that is the problem.

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