Question: RNA-seq illumina paired-end data simulation with fold change differences
1
gravatar for k.kathirvel93
2.3 years ago by
k.kathirvel93260
India
k.kathirvel93260 wrote:

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.

rna-seq sequence simulation • 786 views
ADD COMMENTlink modified 2.1 years ago by grant.hovhannisyan2.0k • written 2.3 years ago by k.kathirvel93260

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

ADD REPLYlink written 2.3 years ago by lakhujanivijay5.2k

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.

ADD REPLYlink written 2.3 years ago by Devon Ryan96k

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by k.kathirvel93260

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

ADD REPLYlink written 2.3 years ago by Devon Ryan96k
0
gravatar for grant.hovhannisyan
2.1 years ago by
grant.hovhannisyan2.0k wrote:

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.

ADD COMMENTlink written 2.1 years ago by grant.hovhannisyan2.0k
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