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
>
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
Then anybody knows how to creat a marker file for GISTIC2?
•
written
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zizigolu
1 answer
The solution was very simple but after contacting GISTIC2 team :)
Supposing you have a segmentation file like this
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
I added the corresponding markers that returns this
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Do you solve this problem of MARKER file? Thx.
How can you get the marker number of rs62635286? Thank you very much.
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
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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.