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!
3 answers
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/
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 :-)
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