Creating marker file for GICTIC2

Question

[zizigolu]

Hi

I have generated a segmentation file (copy number) like this

 > head(segg)
  Illumina_Barcode_ful Chromosome    Start      End Segments_mean number_of_snps
1                t_005          1    13116  2063094     -0.722466            996
2                t_005          1  2065339  5926507    -10.688250           2675
3                t_005          1  5927738 28678709     -0.722466          14307
>

[REDACTED DROPBOX LINK]

I need a marker file for gistic2

Here people say

https://github.com/cBioPortal/cbioportal/blob/master/docs/Data-Loading-Tips-and-Best-Practices.md

http://crazyhottommy.blogspot.com/2017/11/run-gistic2-with-sequenza-segmentation.html

I should create a line for each start and end position. E.g. if seg file contains

  Illumina_Barcode_ful Chromosome    Start      End Segments_mean number_of_snps
         t_005                     1    13116  2063094     -0.722466    996

markerfile this becomes

Marker Name     Chrom   Pos
rs62635286      1            13116
?                   1   2063094

But I don't figure out what they are saying

This is the position of all my markers

[REDACTED DROPBOX LINK]

Then anybody knows how to creat a marker file for GISTIC2?

[Ram]

Please do not share dropbox links. If you wish to share text data, use GitHub gists or paste them directly in your post. I'll be disabling the links in your post.

[tingting.gao]

Do you solve this problem of MARKER file? Thx.

[tingting.gao]

How can you get the marker number of rs62635286? Thank you very much.

[zizigolu]

Hi

They helped me to count the number of markers in each position in this post

https://bioinformatics.stackexchange.com/questions/8531/extracting-the-number-snp-in-each-range?noredirect=1#comment11314_8531

This is my main question

https://bioinformatics.stackexchange.com/questions/7499/getting-this-information-for-gistic2

If you could not solve I will try to help you

[Ram]

Please do not add answers to question **unless you're actually answering the question. Use Comments instead. I'm moving your answers to comments on the top level post for now, but please be more careful in the future.

[tingting.gao]

Hi, Do you have solved this problem of MARKER file? I have the same problem. And could you please tell me how can you get the marker number of rs62635286? Thank you very much.

Answer 1

[zizigolu]

The solution was very simple but after contacting GISTIC2 team :)

Supposing you have a segmentation file like this

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I added start positions afterward the end positions in a column then I added the corresponding chr to another column finally from 1.9 million SNPs file or scanngs output like

[REDACTED DROPBOX LINK]

I added the corresponding markers that returns this

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