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alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
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Gene level expression #17

Closed johnmu closed 9 years ago

johnmu commented 9 years ago

I may have missed this in the documentation. But, in the output is it possible to find the simulated gene level expression given that I input a GTF of transcripts and associated fold changes for those transcripts?

If this is not possible, I guess this only way is to input a GTF of genes instead?

Thanks!

alyssafrazee commented 9 years ago

Do you mean you want the simulated gene-level fold changes? I think you could calculate them based on the input baseline expression and fold change for all the transcripts in the gene. Alternatively, if you wanted to specifically set the gene-level fold changes without inputting a GTF of genes, you could set the fold change to be the same thing for all transcripts in the gene. I wouldn't recommend using a GTF of genes, as the RNA-sequencing process operates at transcript-level (so the simulated data would likely be less noisy than real RNA-seq data).