Interpretation of file wgEncodeCrgMapabilityAlign100mer.bw

[陈大洋]

Dear editor,

I am a student coming from China. My name is Max Chen. I am confused about the interpretation of this document wgEncodeCrgMapabilityAlign100mer.bw in this website( https://genome.ucsc.edu/cgi-bin/hgTables).  I don't know what the four columns mean, especially the third column.  I read the references and explanations, but still don't quite understand.  I hope you have some time to explain it.  thank you in advance.

Good luck.

Yours Sincerely.

[Christopher Lee]

Hello Max,

Thank you for your question about the ENCODE CRG Mappability track. Did you get output from the track for a specific region like the below example and are confused as to the output?

track type=wiggle_0 name="CRG Align 100" description="Alignability of 100mers by GEM from ENCODE/CRG(Guigo)" 
#bedGraph section chr21:32976481-33136142
chr21    33029853    33033699    1
chr21    33033699    33033700    0.5
chr21    33033700    33033701    0.166667

If so, the columns follow the bedGraph format, which is explained here:
https://genome.ucsc.edu/goldenpath/help/bedgraph.html

Briefly, the columns indicate the chromosome, start and end coordinates, and then a value over that genomic range. For more information on what the value means in this case, you can read the Alignability sub-section under the Methods section on the track description page:
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeMapability

If you're question is about something different please let us know and we'd be happy to offer further explanation!

Thanks,

Christopher Lee
UCSC Genomics Institute

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[陈大洋]

Hello Christopher,

  

Thank for your response. I took a closer look at the two links below. I wrote down my explanation.  I hope you can check if it is correct.

For the window:

chr21 33029853 33033699 1

K-mer number:   33033699- 33029853+1= 3847

It means that 3847 k-mers found at the window will uniquely align within the whole genome.

For the window:

chr21 33033699 33033700 0.5

K-mer number: 33033700 – 33033699+1=2

It means that 2 k-mers found at the window will align 2 (1/0.5) regions within the whole genome.

looking forward to your response.

Good luck.

Yours Sincerely.

[Jairo Navarro Gonzalez]

Hello Max,

Thank you for using the UCSC Genome Browser and sending your follow-up question.

It is not necessary to add a base to the start coordinate as bedGraph tracks are half-open coordinates. If you want to learn more about our coordinates system, you can read the following blog post: The UCSC Genome Browser Coordinate Counting Systems.

For the window:

chr21 33029853 33033699 1

K-mer number: 33,033,699 - 33,029,853= 3,846

This means that each base in this range is the beginning of a 100-mer, and if you align each of those 3,846 100-mers to the genome, each of them only maps to a single location. Hence, the entire range gets a score of 1/1, or 1. The bedGraph could instead be written as:

chr21 33029853 33029854 1
chr21 33029854 33029855 1
chr21 33029855 33029856 1
chr21 33029856 33029857 1
...
...
chr21 33033698 33033699 1

But since the 4th column is the same, it can be compressed to a single range.

For this other 100-mer:

chr21 33033699 33033700 0.5

If you take the 100-mer starting in this position and align it to the genome, it will align to two locations, and thus gets a score of 1/2, or 0.5.

If you would like to know more about how this data is generated, you should contact the data provider, Paolo Ribeca:

paolo....@gmail.com

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.

If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genome Browser

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[陈大洋]

Hello Jairo，

Your explanation is the same as my expectations.  I will use it to correct the genome mappability, then to call CNV. I will finish the work one month later. Thank for your help!!

Good luck.

Yours Sincerely.