Comparing Two Transcriptome Assemblies

Question

[biofalconch]

I am fairly new to the field of transcriptomics and am doing a de novo assembly using my data, and since rnaSPAdes is fairly new I decided to give it a shot, but since there is no publication on it yet, i decided to compare it with a Trinity assembly from the same sample. However, I do not know what is the way to go, but I was thinking using FastOrtho and CD-Hit to find how similar they are, maybe some metrics like average transcript length, N50, and so on. Any suggestions on how this should be approached?

Answer 1

[Asaf]

http://www.rna-seqblog.com/comprehensive-evaluation-of-de-novo-transcriptome-assembly-programs-and-their-effects-on-differential-gene-expression-analysis/

Might be useful.

Answer 2

[seta]

For the transcriptome assembly, functional evaluation is more important than other parameters, like N50. So, I suggest to do blastx of the assembly against the closely related species and see how many contigs get the best hit, and also how many full-length contigs exist within the assembly. Also, you can use DETONATE package that specifically developed for evaluation of de novo transcriptome assembly.

Hope this helps.