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Old 01-05-2014, 07:22 PM   #1
vishwesh
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Location: Singapore

Join Date: Nov 2013
Posts: 36
Default 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
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Old 01-05-2014, 11:03 PM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
Default

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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