Question: Merge 2 de novo assembly generated using Trinity?
0
gravatar for nbvasani
3.8 years ago by
nbvasani220
United States
nbvasani220 wrote:

Hi Fellow Users,

In past I have generated transcriptome de novo assembly for plant using trinity and annotated about 90% of assembly. Recently I got RNA-seq data from hiseq illumina of same plant. So this time I mapped new rna-seq data to existing assembly and unmapped reads were extracted.

I used this unmapped reads to generate new de novo assembly using trinity. Finally merged both de novo assembly which were generated using trinity. After thoroughly looking at merged assembly I found out that there were many transcript with same ID but different count number. I think number system while generating transcript is same in trinity assembler.

So my next step is to use different assembler like Velvet/oases in order to get most uses of my existing assembly.

Any suggestion about how can I better use of my existing assembly for new data.

Can I make some changes while running trinity?

Can I used different assembler?

 

I would really appreciate any input.


Thanks in advance.
naresh

 

transcriptome rna-seq assembly • 2.7k views
ADD COMMENTlink modified 3.8 years ago by Prakki Rama2.1k • written 3.8 years ago by nbvasani220
1
gravatar for Rayan Chikhi
3.8 years ago by
Rayan Chikhi1.3k
France, Lille, CNRS
Rayan Chikhi1.3k wrote:

How about doing a single Trinity run using the old data + the new data?

The same advice was given in a related question, worth reading: http://seqanswers.com/forums/showthread.php?t=33452

Another discussion here: Does It Make Sense To Merge Oases Multiple-Kmer Assemblies

And a paper documented an assembly merge (using EvidentialGene): http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091776

I have some doubts that running Trinity on unmapped reads from another assembly would be good practice.

ADD COMMENTlink written 3.8 years ago by Rayan Chikhi1.3k

Thanks Rayan!

Advice on thread is vice-versa.

Thanks for all link and suggestion.

Naresh

 

 

ADD REPLYlink written 3.8 years ago by nbvasani220
1
gravatar for Prakki Rama
3.8 years ago by
Prakki Rama2.1k
Singapore
Prakki Rama2.1k wrote:

Instead of collecting unmapped reads and assembling them, assembling the new data using trinity, and then cluster both the assemblies using the cd-hit-est with certain similarity cutoff might also be option. This way same contigs between two assemblies are clustered and the representative is taken by cd-hit-est.

You can also try to merging the assemblies using CAP3 assembler.

ADD COMMENTlink written 3.8 years ago by Prakki Rama2.1k

Hi Prakki!

Thanks for the suggestion.

The main resion why I didn't want to create new assembly:

1] My previous assembly is 80% annotated.

2] My new RNA-seq data consist of 550million reads and if I use this reads to generate assembly it will used my whole PC memory and will freeze the PC.

Thanks,

Naresh

 

 

ADD REPLYlink written 3.8 years ago by nbvasani220
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