Results of denovo assembly from trinity and velvet.

vishwesh · 01-05-2014, 07:22 PM

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

gringer · 01-05-2014, 11:03 PM

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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01-05-2014, 07:22 PM	#1
vishwesh Member Location: Singapore Join Date: Nov 2013 Posts: 36	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

01-05-2014, 11:03 PM	#2
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	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.