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Old 01-09-2012, 11:03 AM   #1
brachysclereid
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Default who coined RNAseq? RNAseq as an alignment first approach only

Hi,
I have some questions regarding semantics surrounding the term RNAseq:

1. Who coined RNAseq? I was under the impression it was:

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. (2008). "Mapping and quantifying mammalian transcriptomes by RNA-seq". Nature Methods 5 (7): 621–628. doi:10.1038/nmeth.1226. PMID 18516045.

Is this correct?

2. If Mortazavi et al (2008) coined the term then RNAseq refers to a reference genome based approach and not a de novo assembly approach since the technique described in Mortazavi et al purely reference based.

For clarity I think the term RNAseq should be reserved for an alignment based approach. Any thoughts on this?

Last edited by brachysclereid; 01-09-2012 at 11:05 AM.
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Old 01-09-2012, 12:08 PM   #2
Richard Finney
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RNA-seq means sequencing RNA molecules. Alignment or assembly is a post-processing step after the actual RNA-SEQuencing.
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Old 01-09-2012, 01:26 PM   #3
brachysclereid
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Default who coined RNAseq? RNAseq as an alignment first approach only

Yes. The fact that RNA-seq stands for RNA-SEQuencing was not lost to me. However, initially the high depth sequencing reads were aligned to a reference genome and thus RNA-seq became synonymous with an alignment first approach. It was only later that de novo assembly of RNA-seq data was performed routinely. At least from my perspective.
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Old 01-10-2012, 12:17 PM   #4
Zigster
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Yes that's true. If someone says RNA-Seq they are implying something reference-based is being done on the dry side. Someone would have to say de novo transcriptome assembly for me to think otherwise, even though the lab work will be identical.
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