RNA-seq illumina paired-end data simulation with fold change differences

Question

[k.kathirvel93]

Hi EveryOne, I am trying to simulate RNA-seq illumina data for differential expression analysis. I have used FluxSimulator and Polyester, but I need a tool which we can tell to that, these genes should be highly expressed and this should be down regulated.

1. Can i do this with Polyester ? If i can, help me how to do.

2. Suggest me some best tools for my objective.

   Thanks in advance.

[lakhujanivijay]

I have added/removed tags to keep the post relevant. +1 for that question!

[Devon Ryan]

What's the utility in dictating which genes are up-regulated? Such tools are mostly useful for testing program, when you don't really care exactly which genes are up/down-regulated.

[k.kathirvel93]

Hi Devon, Yes i really care about tools only. Because am creating pipeline for specific disease RNA-seq data analysis. I have a list of genes which may up regulated and down regulated in control and diseased state. So i want to simulate RNA-seq data with specified up regulated and down regulated genes.

[Devon Ryan]

I'd just generate a simulation and then change the labels on the output, that'd be simpler.

Answer 1

[grant.hovhannisyan]

Not a direct answer to your question, but here you have a nice and detailed review about NGS simulation tools https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/. You can find there the ones that fit your goal.