Results of velvet and trinity denovo assembly.

[vishwesh]

Hi,
I used trinity and velvet for denovo assembly of RNA seq data of single end short reads of average length of 18-25.
For velvet I get contigs of length 40 to 350 and the number of contigs are more than 10000.
For trinity I get only 3 contigs of length more than 1000.
Here are the commands of velvet and trinity.

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

velvetg directory -cov_cutoff auto -read_trkg yes -amos_file yes

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

Kindly let me know where am I going wrong in trinity.

Thanks.

Regards
Vishwesh