velvet parameter setting

[jjjscuedu]

Dear all,

I am now trying to use the velvet to analysis my RNAseq dataset.

I haven't set the advance parameter yet.

./velveth /diag/home/jjin/rice/leaf/velvet/k35/ 35 -fastq -shortPaired /diag/home/jjin/rice/leaf/leaf_both_output.fastq

./velvetg /diag/home/jjin/rice/leaf/velvet/k35/ -min_contig_lgth 100

For my dataset, the read length is 101, the number of pair end is 63 million for each and about 130million for both ends.

However, I find in the final result:

Final graph has 6616306 nodes and n50 of 35, max 3945, total 136553538, using 0/139438284 reads

It means it doesn't use any reads and n50 is just 35.

Can anyone give me some suggestions how they set the parameter of velvet and get reasonable result?

Thanks!

Jingjing