impact of polymorphism on assembly

[chrisbala]

Hi everyone,

Has anyone assessed the influence of polymorphism (within species) on transcriptome assembly? I have not stumbled upon anything yet.

For example, assembling transcriptomes using Trinity using RNA from multiple individuals...

Thanks!

[chrisbala]

Is it bad form to rekindle an old, unanswered thread?

I'm still curious about how Trinity (and other transcriptome assembly software) handles sequence polymorphism in the RNAseq data.

One way to think about my question is this: Say I can do my a assembly with RNAseq reads from a single sample or multiple samples, which is likely to be better? The multi sample assembly would obviously have more genetic variation (potentially causing assembly issues?), but it would also have a larger number of total reads.

Even more generally, I'd be curious about how polymorphisms are treated in the actual assembly. Are the bases called by consensus? I am pretty sure ambiguity/variation is not part of the output fasta file.