Talk:RNA-Seq

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Sections to add

Agreed on normalization in previous comment. Also need to add allele specific expression, eQTL, and single cell Salubrious Toxin (talk) 01:58, 23 October 2016 (UTC)[reply]

Addition of Processing/Normalization

Perhaps a section can be added on normalization procedures of the count data, produced by the sequencing and mapping of the RNA reads. User:Ansjovis86 19:59, 09 January 2016 (GMT+1)

Ref. #2 [Chu (2012)]

The DOI of ref.2 is not working. — Preceding unsigned comment added by Omermar (talk • contribs) 12:20, 28 November 2013 (UTC)[reply]

Comment-Correction

Why there is a reference (and a whole paragraph description) regarding Asemblathon (1 or 2 it does not matter). Assemblathon clearly refers solely to de-novo genome assemblers and not to RNA assemblers. So the reference and the discussion regarding Assemblathon is confusing and not relevant to the RNA-seq assemblers. --CBouyio 21:59, 20 November 2014 (UTC)

Comment

why does deep sequencing redirect here? —Preceding unsigned comment added by 69.153.134.182 (talk • contribs)

It doesn't. Narayanese (talk) 06:16, 25 September 2009 (UTC)[reply]

Comment #2

The term "post-transcriptional mutations" in first paragraph is probably incorrect, I think "modifications" is meant here. MDonDonDon (talk) 15:16, 8 January 2010 (UTC)[reply]

Question

I acknowledge the importance of this technique. However, I ask myself whether the phrase dubbed "a revolutionary tool for transcriptomics" in the first line is just a little bit too promotional for an encyclopedia? Firefly's luciferase (talk) 04:19, 29 January 2010 (UTC)[reply]

I agree. I also would point out that in the summary at the top and the introduction there is very little information about what RNA-seq actually is, and much more meta-information, sales-pitch promotion, and state of the industry. There is very little science content. Dllahr (talk) 15:44, 28 January 2013 (UTC)[reply]

Done Quote removed. I agree lead needs expanding with overview of method Jebus989 ^✰ 16:04, 28 January 2013 (UTC)[reply]

Further, I've tagged the article for the tone issues you bring up, specifically in the introduction. I'll try to get around to fixing these but will leave the tag in the hope that someone beats me to it. Thanks Jebus989 ^✰ 16:14, 28 January 2013 (UTC)[reply]

Helicos bankrupt

In the direct RNA sequencing section, the technology is described as under development by Helicos Biosciences, which is now out of business, as a look at the wikipedia page for the company shows. Reference should be made to another entity developing the technology. — Preceding unsigned comment added by 140.107.111.22 (talk) 23:14, 20 November 2013 (UTC)[reply]

This seems too human focused for a general RNAseq page. For example, statistics are given on the human genome---either say "for example" when giving human genome stats or (better) provide a less human-centric view of RNAseq — Preceding unsigned comment added by 2607:FE28:10:2006:0:0:0:235 (talk) 21:09, 16 December 2013 (UTC)[reply]

Ambiguous statement

In the second paragraph of the introduction, first sentence : "One deficiency with microarrays that makes RNA-Seq more attractive has been limited coverage; such arrays target the identification of known common alleles that represent approximately 500,000 to 2,000,000 SNPs of the more than 10,000,000 in the genome." What genome ? Please specify. — Preceding unsigned comment added by 79.83.73.240 (talk) 07:07, 27 April 2014 (UTC)[reply]

Loss of Handedness due to reverse transcription?

The article says that cDNA synthesis leads to a loss of handedness ("Reverse transcription results in loss of strandedness, which can be avoided with chemical labelling"). Why? If only first strand cDNA synthesis is undertaken, then all the cDNA will be complementary to the RNA, won't it? I think this may have something to do with the synthesis of a second cDNA strand, but that is not what is written in the article. Could someone who understand RNA-seq better than I do please clarify? Marchino61 (talk) 03:04, 9 May 2018 (UTC)[reply]

Thanks for pointing this out Marchino61! I wrote that section and just clarified that cDNA amplification is actually the cause. Salubrious Toxin (talk) 14:07, 23 May 2019 (UTC)[reply]

Unclear what is this

I only have a pop science understanding of this topic, and I would like some clarification here for people like me. I feel like "genetic sequencing" is a concept which many people know, but there is no Wikipedia article for that topic. There also is currently no article on the general concept of RNA sequencing, but RNA sequencing redirects here, even though it seems like this article covers one particular technique of RNA sequencing and not the general concept.

I checked in the edit history and various people have posted various alternative titles for this. Before I just edited this article, the title was just "RNA-Seq" and the usual first-sentence definition was omitted. I added that this technique is also called "RNA sequencing", but wrote in a way to communicate that this is just one technique of RNA sequencing, and that there are others, and this article is only about the popular technique. Elsewhere in the article history someone called this "whole transcriptome shotgun sequencing (WTSS)".

Can anyone clarify how this article relates to the general concept of RNA sequencing? Thanks. Blue Rasberry (talk) 17:46, 7 February 2020 (UTC)[reply]

RNA sequencing

RNA sequencing is redirected here, but as far as I can understand the article is about one specific method. Probably there should be another article, explaining RNA sequencing as a concept. --Hjordmån (talk) 17:03, 18 November 2021 (UTC)[reply]