Question: Does read-depth refer to a fold?
0
gravatar for mangfu100
4.5 years ago by
mangfu100680
Korea, Republic Of
mangfu100680 wrote:

Hi.

In next generation sequencing field, we can easily see the read-depth concept. And I already understand the concept of it. But what is a fold concept?

just look at the below sentence to better explain word 'fold'.

"the average read depth used in the project has increased by 3-fold. At the same time, the number of reads is reduced by 3-fold to yield comparable sequence coverage."

I suppose that fold refers to a measurement of something. Is it right?

I am so puzzled.

sequencing next-gen genome • 1.7k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 4.5 years ago by mangfu100680
1

As written, that passage is illogical. I suspect they meant that read lengths increased 3 fold (possibly from 50bp to 150bp), which allowed for decreasing the total number of reads while maintaining the same resulting coverage. That would at least make sense.

ADD REPLYlink written 4.5 years ago by Devon Ryan89k

Yeah, it looks like they did something other than just increasing # of reads to increase the read depth (maybe they had a lot of garbage reads before, and fixed that, or maybe they are trying to get reads that align to a target region, and greatly increased their specificity), and once they increased the proportion of desired reads 300%, they scaled back the total # of reads to 33%, yielding the same amount of data for less reagent cost.

ADD REPLYlink written 15 months ago by swbarnes25.2k

Hello mangfu100!

We believe that this post does not fit the main topic of this site.

Whilst this question veers a little closer to bioinformatics relevance, you still do seem intent on using BioStars to clear points of grammar that are easily solved with a quick Google search!

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.5 years ago by Daniel Swan13k

I don't know Daniel, I am with the OP here - the sentence in question is very confusing (and probably inaccurate) and I don't think it has to do with having English as a second language (perhaps the authors of the sentence are at fault)

The sentence appears to state that  they have reduced the number of reads by a factor of 3 yet still managed to increase the coverage 3 times over. How would that even be possible? I don't really get it.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Istvan Albert ♦♦ 80k
5
gravatar for Renesh
4.5 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

They are not same. The read depth means how many times bases are sequenced compared to target. The fold means change in number in two states. For example, In gene expression analysis, the fold change means change in read count in control and treatment sample. If its is changed by 2 factor, we can say fold change of 2 (control-10 and Treatment-20).

For your case, the number of bases sequenced increased by 3 times (3-fold) as compared to old one (previous 1M and Later= 3M).

ADD COMMENTlink written 4.5 years ago by Renesh1.6k
1
gravatar for toni
4.5 years ago by
toni2.1k
Lyon
toni2.1k wrote:

No. You should rather see this as a multiplicative factor. Increased by 3-fold means : NEW = 3 * OLD

 

 

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by toni2.1k
1
gravatar for Michael Dondrup
4.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

https://en.wikipedia.org/wiki/Fold_change

ADD COMMENTlink written 4.5 years ago by Michael Dondrup46k
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