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  • Analysis transcriptome 454 + sanger

    Hi all

    I'm starting a transcriptome analysis using data from 454 and Sanger. I want to create a reference transcriptome (no genome information), what do you recommend me? Assemble data separately and then assemble the contigs or try a hybrid assembly.

    Regards

  • #2
    The 454 assembler (Newbler) can accept use extra Sanger reads in the assembly. You just need to ensure you put the correct headers in the .fasta/.qual files (eg. "template=XXXX dir=X library=XXX"). Don't forget to run it in "cDNA" assembly mode too.

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    • #3
      Thanks

      I've tried with similar percentages of 90 and 95%, but only 67% of the sequences are assembled, i'll try moving some parameters to increase the number of reads assembled.

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