Aedes vexans RNA-seq de novo assembly

Question

[fluentin44]

Hi all,

Does anyone have reccomendations for RNAseq sequencing depth where the transcriptome will require de novo assembly? It would be on the Aedes genome, ive not seen anything catagorical beyond 50-100 million read pairs (100 - 200 million total).

Thanks, Matt

[GenoMax]

More would always be better but at some point budget reality will kick in.

Looks like there is already a publication on this topic: https://doi.org/10.1111/1748-5967.12440

[Brian Bushnell]

The number of read pairs is not the most relevant number; it's the depth that matters. You will be able to assemble most of the genes that are 5x+ and you won't be able to assemble the ones that are under ~2x. So, it depends on the relative expression.

Depending on the organism, artificially depleting certain genes like ribosomes or albumin can be helpful to increase the abundance of informative sequences. I don't have any experience with mosquitoes but albumin is definitely a problem with human RNA-seq, and ribos are a big problem with bacterial RNA-seq. Whenever you want to do an experiment with a minimal amount of sequence, it's useful to artificially deplete sequences you know will be overexpressed ahead of time.