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XSQ format compatible denovo Transcript Assemblers

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  • XSQ format compatible denovo Transcript Assemblers

    Hello all,
    We are working with SOLiD 5500 System. We want to assemble our denovo transcripts for a plant. We have come across a few assemblers compatible with XSQ format but we still need a good advice on XSQ compatible denovo transcripts assemblers. Thankyou.
    Last edited by Zainab; 08-03-2016, 05:30 AM.

  • #2
    I don't know of anything here. de novo assembly is very tricky with SOLiD and actually doesn't work at all. You can expect very short transcript fragments (<1kbp, most ~200bp). Illumina works a lot better here.

    I haven't tried it, but it might make more sense to map to a reference genome and then attempt to use cufflinks on the BAMs. Not de novo I know, but it might be more rewarding.
    Last edited by colindaven; 08-03-2016, 11:13 PM. Reason: more info

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