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  • Mapping HiSeq to Proteins

    I've got a project with a tight deadline that will include needing to map some RNASeq data to a reference.

    There is a reference transcriptome "published", but only the protein sequences are available, not the DNA.

    Does anyone know of any tools that will let me map my fastq files to a protein reference? I've been searching around, but might get an answer faster this way

    Right now I'm thinking (dreading?) I may need to do a fastq-to-fasta and use exonerate.

    Thanks for any ideas.

  • #2
    Why not perform a de novo assembly with your RNAseq data instead?

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    • #3
      That is running but will likely take a couple of days, which is part of why I was looking for an alternative approach.

      Plus now I'm simply curious - is there a tool out there that will let you make RNASeq reads to a proteome?

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      • #4
        Check out blat.
        Blast can do it , too.

        *at least I think they do*

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