Tools For Saturation Analysis Of Rna-Seq Experiments

Question

[samsara]

I have never worked with RNA-seq analysis before. I am looking for some tools for saturation analysis of RNA-seq experiments meaning finding out at which amount of reads we do not find more expressed genes.

Answer 1

[Asaf]

I didn't quite understand what exactly you're trying to find but a great place to start with the world of RNA-seq mapping is with this exercise of mapping RNA-seq to the genome using Galaxy: https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise This is just an appetizer, You'll have to study the tools in-depth if you would really want to use them.

[KCC]

I think the OP is looking for tools that tell them if they have found the majority of expressed reads. In other words, how deeply do they need to sequence to find all the expressed genes.

Answer 2

[Wrf]

this was discussed somewhat here:

How Much Coverage Do We Need For An Rna-Seq Experiment?