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  • Results of denovo assembly from trinity and velvet.

    Hi,
    I used velvet and trinity for denovo assembly for RNA seq of short single end reads of length between 18 to 23. But the results that I got from velvet and trinity are different.
    In velvet I get contigs of length between 40 and 350 and the no of contigs is more than 20000.

    In trinity I get only 3 contigs of length more than 1000.

    Here is the velvet and trinity command that I used.
    velvet
    ./velveth directory 17 -sam -short '/home/xxx.fastq'
    ./velvetg directory -cov_cutoff auto -read_trkg yes
    Trinity
    Trinity.pl --seqType fa --JM 10G --single /home/xxx.fasta --CPU 2

    Can somebody tell me what parameter am I missing in trinity.

    Thanks.

    Vishwesh

  • #2
    Trinity needs reads of at least ~50 to be effective, because it needs a kmer at each end of the read in order to join -- I think more recent versions have relaxed this requirement a bit, but it's still a reasonable minimum target length. You're not going to get anything much useful out of Trinity with short reads.

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