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

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.

sequence simulation rna-seq
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updated by grant.hovhannisyan grant.hovhannisyan • written by k.kathirvel93 k.kathirvel93

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

• 1 views • link
written by lakhujanivijay lakhujanivijay

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.

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written by Devon Ryan Devon Ryan

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.

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written by k.kathirvel93 k.kathirvel93

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

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written by Devon Ryan Devon Ryan

1 answer

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.

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written by grant.hovhannisyan grant.hovhannisyan

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