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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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Getting prob number and segment mean from scatncg copynumber #84

Open beginner984 opened 5 years ago

beginner984 commented 5 years ago

Sorry Long time I am struggling how to provide GISTIC required input like Num_Probes and Segment_Mean

I have called somatic copy number by scatngs and I have copy number output file (attached); In scatngs reference paper says in this file we have

  Segment number

    Chromosome

    Start position (origin-1)

    End position (origin-1)

    Major copy number—normal

    Minor copy number—normal

    Major copy number—tumor

Minor copy number—tumor

I am wondering how I can get

Num_Probes and Segment_MeanFrom this file? People say

Segment_Mean = log2(tumour copy number / 2) So, does that mean I should add up Major copy number—tumor and Minor copy number—tumor to get tumour copy number? for getting Num_Probes what should I do?

Any help please?

Thanks a lot in advance

RamRS commented 5 years ago

Please do not open GitHub issues for these sort of questions. You're already asking bioinformatics SE for help, do not open GitHub issues for issues that are not related to the tool's functionality.

beginner984 commented 5 years ago

But I am not finding the answer of this question anywhere in google :(

RamRS commented 5 years ago

That does not mean GitHub is the place to discuss this problem you're facing, especially given it's a problem you're having trying to extract something for a downstream step. Think about it this way - you should be using a GitHub issue to produce a bug report for a problem that you could solve by changing the tool's source code. Is this such a problem?