simulate rnaseq reads from ref. genome

Question

[grant.hovhannisyan]

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

Answer 1

[GenoMax]

randomreads.sh in BBMap suite 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.

[Botond Sipos]

Gffread can extract the transcripts for you.

[grant.hovhannisyan]

Hi genomax, Thanks, and yes, basically I need reads from coding region to simulate RNAseq data. As far as I know, randomreads.sh generate reads from reference sequence, so in my case I'd have to extract transcriptome from genome and then feed it to randomreads.sh, is that correct?

[GenoMax]

Yes. If you have the GTF/GFF available then use @Botond's solution to get the reference transcriptome.

[grant.hovhannisyan]

Great, thank you both!