Hi Biostars,

My question might be a duplicate, but what software would you recommend to simulate RNAseq reads (with different parameters like read length, PE/SE, error-rate, strandedness, etc), by using reference genome and annotations as input.

Google search and omicstools give many results, but I didn't find any soft so far fitting to my needs.
ART looks good (but not specific to RNAseq), and I bet that there would be something in BBtools :)

Would appreciate any comments and suggestions.
Thanks 
`randomreads.sh` in [BBMap suite][1] will do what you want. 

I assume you want to generate reads only from the transcriptome (i.e. provide a milti-fasta of transcripts. Don't think of any programs that can take ref genome+GTF file)? Otherwise there is nothing special about RNAseq as far as read generation would be concerned.


  [1]: https://sourceforge.net/projects/bbmap/