transcriptome assembly evaluation

Question

[dovah]

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!

Answer 1

[Carlos Caicedo]

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

Answer 2

[Sej Modha]

You could use transrate for assembly evaluation.

Answer 3

[BioBing]

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 :-)