GC model file

Question

[hoseinsalehian6]

Hi I need to GC model file for adjust Genomic wave in result of penncnv software also I dont know commands for this in linux.

[hosin]

Hi I need to a GC model file for adjust Genomic wave in result of penncnv software.my data is about ovine high- density 600k chip, so it doesnt worked with GCmodel in software package because it is for human data.

[Kevin Blighe]

Did you just create an extra account?

[Kevin Blighe]

This script, part of PennCNV, can apparently generate a GCmodel file for you: https://github.com/WGLab/PennCNV/blob/master/cal_gc_snp.pl

Please take a look.

Edit: I also recommend that you contact the PennCNV developers and / or Affymetrix, as they may be able to quickly supply this file to you

[Kevin Blighe]

I have added to my answer (below), effectively showing you exactly what you need to do

Answer 1

[Kevin Blighe]

Please take a look at the example here: GCmodel adjustment. The GCModel file should come with the package when you download it.

If the GCModel file does not exist, then take a look at the FAQ in order to see how you could produce one:

1. How to use genomic wave adjustment independent of CNV calling?

Some users just want to adjust signal intensity values, without generating CNV calls by PennCNV. The genomic_wave.pl program in PennCNV package can be used to adjust signal intensity values. The input file must have a field in the header line that says "*.Log R Ratio". The -adjust argument can be used to generate a new file with updated Log R Ratio measures. This procedure can be also used in Agilent arrays or Nimblegen arrays for adjustment. Use the cal_gc_snp.pl script to generate GC model file for these custom arrays.

[source: http://penncnv.openbioinformatics.org/en/latest/misc/faq/]

[Kevin Blighe]

To further assist you:

In order to create your own GCmodel file, you need three things:

1. cal_gc_snp.pl script from GitHub
2. GC content information for ovine (Ovis aries)
3. SNP marker information

------------------------------

cal_gc_snp.pl can be downloaded from PennCNV's GitHub page: https://github.com/WGLab/PennCNV/blob/master/cal_gc_snp.pl

GC content information for ovine is available from UCSC for build1 and build3 of the sheep genome:

• http://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/gc5Base.txt.gz (buiid 1)
• http://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/gc5BaseBw.txt.gz (build 3)

Once you download these, unzip, and then sort (and save a new copy) using: sort -k 2,2 -k 3,3n <input > output

The SNP file you should already have for your microarray version. It needs to be of the form:

Name            Chr     Position
rs1000113       5       150220269
rs1000115       9       112834321
rs10001190      4       6335534
rs10002186      4       38517993
rs10002743      4       6327482

---------------------------------------

You then generate the GCmodel file with:

perl cal_gc_snp.pl gc5BaseBw.sorted.txt SNPfile.txt -output ovine.gcmodel

[bjwiley23]

For the SNP6 array, does anyone know where to find the snpfile? Thought it might be in the gw6 folder from PennCNV at this link below but not there. http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz

Nevermind you can just get from UCSC table browser.

[dr.fakharunnisa]

Thank you for your wonderful explanation. Can you please guide, from where i can take the GC content information of cattle genome?