Shulou(Shulou.com)06/01 Report--

This article introduces the relevant knowledge of "how to use circos zooms". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

In the display of chromosome information, if you want to focus on the information of a certain region, you can use zooms to achieve. Zooms acts as a telescopic function to enlarge or shrink the original area.

The configuration file is written as follows:

Zooms consists of multiple zoom, and each zoom must have the following parameters

Chr

Start

End

Scale

The three parameters chr, start, and end specify the region of the chromosome to be scaled, and scale specifies the multiple to be scaled.

Look at a specific example:

In the diagram above, multiple regions of the chromosome are scaled. Among them, some regions on chromosome 1 are enlarged and some regions on chromosome 2 are reduced.

The 120Mb region of chromosome 1 is magnified by 2 times, and the next region is magnified by 3 times, 4 times and 5 times, respectively.

The 100-120Mb region of chromosome 2 is reduced to 0.5 times that of the original, and the following regions are reduced to 0.25, 0.1, 0.25 and 0.5, respectively. The corresponding configuration file is written as follows.

In the above example, there is no overlap between the areas that need to be scaled, and when these areas overlap later, the scaling ratio of the overlapping area is the highest. For example, the following scale

The actual processing will be scaled as follows

For areas that are not in dispute, they are scaled according to the specified scale, and for overlap areas where multiple scaling ratios are specified, the maximum value is used as the final scale.

Among the parameters related to zoom, there are two very special parameters.

Smooth_distance

Smooth_steps

It is written as follows:

The purpose of these two parameters is to control the scaling of adjacent areas. When these two parameters are not specified, only the target area is scaled; when these two parameters are specified, the upstream and downstream areas are scaled.

Smooth_distance controls the distance between the upstream and downstream areas that need to be scaled. 2R represents twice the target area. Since the target area is 120u to 125u and the length is 5m, the upstream and downstream areas that need to be scaled are 2 X 5 = 10m. These areas also need method scale multiples. Smooth_steps controls the scaling steps of the upstream and downstream regions, and the scaling ratio of the upstream and downstream regions is a linear growth relationship. In the following diagram, we can see that the 10m region upstream of the target region of chromosome 1 is also magnified by 10 times. The scaling is not directly magnified 10 times of the whole region, but is divided into 10 sub-regions, and the scaling ratio of each region is gradually increasing. 1.8 increases to 9.2, which adds up to 10 times the original amount.

For zooms, there are only 6 parameters, and the specific meaning is also explained in detail above. But for chromosome scaling, besides zooms, there are other parameters that can also be realized.

1. Scale the entire chromosome

This is achieved through the chromosomes_scale parameter, written as follows

Chromosomes_scale = hs1:0.2;hs2:0.2;hs3:0.2;hs8:5;hs9:5;hs10:5

Hs1:0.2 says that chromosome 1 will be reduced to 0.2 times the original size, and the scale of each chromosome will be separated by semicolons.

two。 Scale part of the chromosome

It is written as follows

Chromosomes = hs1 [a]: 0-20th HS2 [b]: 0-20th HS1 [c]: 20-40th HS2 [d]: 20-40th HS1 [e]: 40-60th HS2 [f]: 40-60

Chromosomes_scale = aVaVOTIBRATION 0.5 BUBUR 0.5 BUBUR 5 ETHING 5

Take hs1 as an example, in chromosomes, three intervals a, c, e are specified, and in chromosomes_scale, these three intervals are scaled.

That's all for the content of "how to use circos zooms". Thank you for reading. If you want to know more about the industry, you can follow the website, the editor will output more high-quality practical articles for you!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.