transcriptome assembly evaluation
3
1
Entering edit mode
6.4 years ago
dovah ▴ 40

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!

Assembly transcriptome • 1.8k views
ADD COMMENT
3
Entering edit mode
6.0 years ago

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 COMMENT
1
Entering edit mode
6.4 years ago
Sej Modha 5.2k

You could use transrate for assembly evaluation.

ADD COMMENT
0
Entering edit mode
6.0 years ago
BioBing ▴ 150

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 COMMENT

Login before adding your answer.

Traffic: 2235 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6