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
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grant.hovhannisyan
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.
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?
Great, thank you both!
Gffread can extract the transcripts for you.
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