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  • Blasting human SOLiD short reads against human genome reveals no sig results

    I have converted SOLiD SRA to fasta using fastq-dump.

    Then, I used the Galaxy groomer to remove the adapter. After that, I wrote a script to translate "0123." to "ACGTN" in the fasta file.

    Then, I tried blasting that fasta file against the human genome, and found no significant results.

    Earlier, my SAM alignment (derived from the converted fasta file and a reference .mrna human file) also showed very few hits (only 406 out of 6 million).

    So, now the finding from BLAST makes me think that the conversion of the human SOLiD sra file went awry somewhere.

    I got my .sra file from here (http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR452364, by downloading the "Run" HTTP file).

    Based on the above information, does anyone have any ideas where I went wrong in converting the SOLiD sra file to a format ready for BLAST/SAM?

    Many thanks...

  • #2
    lanner,

    You can't translate colorspace to base-space like that, even though the reads give you the first letter. It can only be done after mapping because of Solid's incredibly high error rate - everything after the first error will be wrong.

    Of course, it WOULD work for error-free reads, and there should be a few... so try searching for the absolute highest-quality reads, and you might be able to translate and blast those.

    Comment


    • #3
      It would not work even for error free reads since he is not converting from colorspace to basespace.

      Comment


      • #4
        Thanks Brian and Chipper. I realize now that basespace to colorspace conversion is much more difficult than just a string translation!

        Comment

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