Tools for generating realistic rna-seq reads from reference transcriptome
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7 weeks ago
Jjbox ▴ 30

Hi Biostars,

I am interested in generating realistic rna-seq. Does anyone know tools that use 1) reference transcript and 2) isoform expression as input and then genreate realistic rna-seq? By meaning reference transcript, I am referring to this here (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml).

Imagine the top blue bar is the reference transcript. Would there be such tools or ways to generate the realistic rna-seq reads (the small bar with red head and tail)?

enter image description here

reference reads rna-seq transcriptome • 325 views
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Any read simulation tool should work. ART(https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm ) randomreads.sh from BBMap suite are a couple of examples.

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Hi Thanks! I am trying to understand this link. Are you saying using reference transcripts as an input, I can get rna-seq data from this tool?

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7 weeks ago
af1065 • 0

There is the Polyester R package.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635655/

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Hi thanks a lot! It looks like polyester takes transcript reference as input and make rna-seq reads. Do you know any new libraries?

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