Question: The best factors to evaluate the quality of de novo transcriptome assembly
2
gravatar for seta
4.4 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi everybody,

There are different criteria to evaluate de novo transcriptome assembly quality, which all of them have their pros and cons. What are the best and time-consuming way to assess quality of de novo transcriptome assembly to make a reliable transcriptome assembly. Please share me your experiences, any comments warmly welcomed. thanks

 

 

 

 

 

 

 

 

sequencing rna-seq assembly • 2.1k views
ADD COMMENTlink modified 3.0 years ago by Antonio R. Franco4.0k • written 4.4 years ago by seta1.1k
3
gravatar for rtliu
4.4 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

"Transrate analyses a transcriptome assembly in three key ways:

  1. by inspecting the contigs themselves
  2. by mapping reads to the contigs and inspecting the alignments
  3. by aligning the contigs against proteins from a related species and inspecting the alignments

By far the most useful metrics are those based on read mapping, in particular you should pay attention to the Transrate score and the individual contig scores."

If you've got Ruby v2.0.0 or later, install Transrate with the command: $ gem install transrate

I have not tested transrate yet, but it is high on my 2015 Todo list.

 

ADD COMMENTlink written 4.4 years ago by rtliu2.0k

Hi rtliu,

Many thank for your response. It sounds great, is there anybody who tried this tool? 

ADD REPLYlink written 4.4 years ago by seta1.1k
0
gravatar for Antonio R. Franco
3.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

If a truly de novo transcriptomic assembly in an organism lacking of reference genome needs to be evaluated, test Detonate

ADD COMMENTlink written 3.0 years ago by Antonio R. Franco4.0k
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