Generating realistic rna-seq using polyester from reference transcript

[jjbox]

Hello everyone,

I am quite new to using polyester and would like to gain some insights from the expert when using it for my experiment. If you can help me answer my question, that would be great!

I want to generate one file that contains realistic enough rna-seq from the reference transcript. It would be nice for this realistic rna-seq to be Illumina profiled, introducing hexamer bias, and positional bias.

I had trouble understanding polyester since there is an input called "fold_changes" that generates multiple files. Could anybody give me a suggestion for a command line to make one output file that contains all the biases so that it can be realistic enough? I wasn't sure how much bias should be added to be realistic, so it would be nice to be an Illumina profiled with the biases I included above.

Thanks in advance!