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  • vishwesh
    Member
    • Nov 2013
    • 39
    #1

    Trinity parameters missing.

    Hi,
    I used both Trinity and velvet for denovo assembly for RNA seq data. In velvet I get contigs of length between 40 and 350.
    But in Trinity I get only 3 contigs of length more than 1000.
    Here is the parameters of velveth and velvetg.

    ./velveth directory 17 -sam -short '/home/...L006_merged.fastq'

    ./velvetg directory -cov_cutoff auto -read_trkg yes -amos_file yes

    for trinity
    Trinity.pl --seqType fa --JM 10G --single /home/../xxx.fasta --CPU 2

    Kindly let me know what parameter am I missing in trinity.
    Thanks.
    Regards
    Vishwesh
    Tags: None
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