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Why does SHRIMP hate my fastq?

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  • Why does SHRIMP hate my fastq?

    Hello everyone,

    I'm trying to run SHRiMP to align my SOLiD reads in colorspace to a reference genome. I put the .csfasta and .qual files together myself, tried with and without a leading "!" quality, but it seems like SHRiMP does not like my csfastq input.
    I keep getting the following error message when running the following command:

    gmapper-cs --fastq combined_Library33_33_F3.csfasta.csfq NC_009641.fa > combined_Library33_33_F3.csfq.sam

    error: invalid character in input file [combined_Library33_33_F3.csfasta.csfq]
    (Did you mix up letter space and colour space programs?)

    Any idea what is the problem here? Can you run SHRIMP with fastq files in colour space or only with fasta files?

    Below I pasted 2 of the reads that I'm trying to align (also tried it with "!" as the first quality score)...

    thanks


    Code:
    >01_3_196_F3
    T101323230120313102033232221322013101323221102200312031332312230331301221111
    +01_3_196_F3
    KKKKKKKGKKEGDGGCDHHHGHDHGADGGEDGGGI?GADA5?D5C5D9A<(??9((<9A<5??95,55,1,5199
    >01_3_804_F3
    T121130212230300233301032121131011300300221233121130033021031002101322321022
    +01_3_804_F3
    IIFFFHH?D1<[email protected][email protected]@DDFGFFD<[email protected][email protected]@[email protected]@5<55,,5591050,<1

  • #2
    Try changing the ">" to "@" before the read name

    Comment

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