Hi all,

I am quite new to using polyester and would like to gain some insights from the expert when using it for my experiment.

I want to generate one file that contains realistic enough rna-seq from the reference transcript here (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml#:~:text=gff3-,RefSeq%20Transcripts,-Fasta).

It would be nice for this realistic rna-seq to be Illumina profiled, introducing hexamer bias, positional bias, and SNP (indels). I had trouble understanding polyester, since there is an input called "fold_changes" that generates multiple files. Could you 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!