Question: transcriptome assembly evaluation
0
gravatar for dovah
2.6 years ago by
dovah30
dovah30 wrote:

Hi all.

I would like to compare a de-novo (Trinity) and a reference-based (Cufflinks) Illumina assembly, done on the same dataset (organism D. melanogaster). You know how should I proceed? I am particularly interested in detecting splice variants.

Many thanks!

transcriptome assembly • 958 views
ADD COMMENTlink modified 2.2 years ago by BioBing100 • written 2.6 years ago by dovah30
3
gravatar for Carlos Caicedo
2.2 years ago by
Colombia/Universidad de Antioquia
Carlos Caicedo130 wrote:

Hi dovah

You can use Transrate, Detonate, rnaQUAST and SCAN (Sequence Comparative Analysis using Networks). rnaQUAST and SCAN need a reference to evaluate the assembled transcriptome. Detonate and Transrate are free-reference but also can work in a "reference-based" mode.

These are the links if you want to download the software mentioned above.

http://hibberdlab.com/transrate/

http://deweylab.biostat.wisc.edu/detonate/

http://bioinf.spbau.ru/en/rnaquast

http://evol-net.fr/index.php/en/downloads

ADD COMMENTlink written 2.2 years ago by Carlos Caicedo130
1
gravatar for Sej Modha
2.6 years ago by
Sej Modha4.2k
Glasgow, UK
Sej Modha4.2k wrote:

You could use transrate for assembly evaluation.

ADD COMMENTlink written 2.6 years ago by Sej Modha4.2k
0
gravatar for BioBing
2.2 years ago by
BioBing100
Denmark
BioBing100 wrote:

You can also run a BUSCO analysis on the two assemblies (to test the "completeness"): http://busco.ezlab.org/

I like Detonate (suggested by Carlos Caucedo) to compare my transcriptome assemblies :-)

ADD COMMENTlink written 2.2 years ago by BioBing100
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