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  • RyNkA
    Member
    • Jul 2013
    • 20

    #1

    de novo assemly of Oases resulted in very high length transcript

    As title, I was trying to do a multi kmer approach of Velvet/Oases on RNA seq data (single end read)

    So I run Velvet and then oases, what I found out is that the transcripts.fa final file consist of a few contigs like this example

    >Locus_1_Transcript_62758/62767_Confidence_0.018_Length_270364
    GCGGCGTTCACCACTAGTCTTCCTCGCAAGCGCTCTGGCGTGGGCCTCCTTCTTTCAACT
    TCATGGAAGGTGATGAGGTGGTCATAGTCAAAGGTATTGTCGATGTCTCTAACTTCATGG
    AAGTCCATCCTGTCCAACCTGTTCCATCCTGGCGAGATCTTCAGCACAGCGTCGTCCTCC
    TGAATGTGCTGTCTCTCATGTCGTTCGATCCTACCGCTGAGACCTAGACACAACCTTAGT
    ATGTGATCAGCCTCTGACCTTTGGAGGAATTGAGGTGCTTATAGGCATGGTCCCTTGATA
    AGAGACCGGTATCTCCAGCATATCCTTGGCATGATCCGCGTTCATGAAGAGACGGTATCC

    So a transcript with a length of 270.000bp ? It also contains lots of N's inside. (through velvet final file *contigs.fa as well as the raw data do not have any N's)

    *** I read somewhere on the seqans and found out that the oases algorithm try to do scaffolding even if there is no pair end read is available, that maybe the cause to the N's in the result transcripts.fa file

    Any suggestions ?
    Last edited by RyNkA; 05-01-2014, 04:51 PM.

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