Question: simulate rnaseq reads from ref. genome
1
gravatar for grant.hovhannisyan
12 months ago by
grant.hovhannisyan1.3k wrote:

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

rna-seq bbtools simulation • 396 views
ADD COMMENTlink modified 12 months ago by genomax59k • written 12 months ago by grant.hovhannisyan1.3k
1
gravatar for genomax
12 months ago by
genomax59k
United States
genomax59k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax59k
1

Gffread can extract the transcripts for you.

ADD REPLYlink written 12 months ago by Botond Sipos1.7k

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?

ADD REPLYlink written 12 months ago by grant.hovhannisyan1.3k

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

ADD REPLYlink written 12 months ago by genomax59k

Great, thank you both!

ADD REPLYlink written 12 months ago by grant.hovhannisyan1.3k
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