Trinity parameters missing.

[vishwesh]

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