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  • Annotations using GS Mpper

    I am using GS mapper for mapping reads to reference. I was wondering whether some one has already done the annotation of the reads using GS Mapper. I usually use our in-house wrapper annotation tool to do this.

    The manual says that "-fd" OR "-annot" option can be used to annotate the reads/run while running GS Mpper. But I always get an error while using these options.

    Is the mapper looking for a specific format?

    Thanks.

  • #2
    Originally posted by pmishra1982 View Post
    Is the mapper looking for a specific format?
    Think it wants GoldenPath format, IIRC.

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    • #3
      Thanks for the reply.
      But the manual says that it looks for refGene.txt file. Is there a free software to convert GFF file to the GoldenPath file format ( I guess its called AGP file).

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      • #4
        The refGene.txt file format refers to the file which corresponds to the UCSC Table Browser refGene table. Here is a link to the table schema description: http://genome.ucsc.edu/cgi-bin/hgTab...e+table+schema

        I don't know of any scripts available to convert a GFF file to this table format.

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        • #5
          @kmcarr:Thanks for the format.
          I looked into the UCSC browser description but this is mostly for Human genomes. I am working on Ricketssia. Generally I use our in-house wrapper to give me annotations which outputs in the standard Genbank format. So to get the exons and other information, I have to run it through something like GENSCAN? Has any body worked on bacteria to extract annotations directly from the 454 data using GS Mapper?

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