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  • Mapping cDNA's to assembly

    I've got a partial assembly of a low coverage genome (about 250k contigs) and a set of assembled cDNAs I'd like to map to those contigs to get a first guess as to where the introns lie, etc-. Is there a nice piece of software that'll do that relatively quickly? I suppose I could do it with several rounds of blast, or even script a pipeline that makes a blast DB from each assembled genome contig and runs the cnda against it, but I figured I'd ask here first. Visualization would also be a nice plus...

    Thanks!

  • #2
    Blast would be an option and you can then use the script blast2sam.pl from samtools to get the sam version and vizualise with IGV

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    • #3
      I find BLAT has a better understanding of spliced alignments

      I use Don Gilbert's blat2gff.pl and view in gbrowse
      --
      Jeremy Leipzig
      Bioinformatics Programmer
      --
      My blog
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      • #4
        Don't know if it's relevent but I just read the BWA for long read paper. you could have a look at that

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        • #5
          mgalign also has a much better understanding of spliced alignments than BLAST.

          http://proline.bic.nus.edu.sg/mgalign/mgalignit.html

          I used this to annotate a velvet assembly and was quite pleased at the results. The output is easily translated to genepred or bed formats.

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