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
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
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