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Creating marker file for GICTIC2
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12 months ago
F ♦ 3.4k
Iran

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?

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Entering edit mode
12 months ago
F ♦ 3.4k
Iran

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

Supposing you have a segmentation file like this

[REDACTED DROPBOX LINK]

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

[REDACTED DROPBOX LINK]

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