Question: GC model file
0
gravatar for hoseinsalehian6
3.1 years ago by
hoseinsalehian60 wrote:

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.

genome • 1.8k views
ADD COMMENTlink modified 3.0 years ago by Kevin Blighe71k • written 3.1 years ago by hoseinsalehian60

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.

ADD REPLYlink written 3.0 years ago by hosein_salehi60

Did you just create an extra account?

ADD REPLYlink written 3.0 years ago by Kevin Blighe71k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Kevin Blighe71k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Kevin Blighe71k
1
gravatar for Kevin Blighe
3.1 years ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k wrote:

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/]

ADD COMMENTlink written 3.1 years ago by Kevin Blighe71k

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:

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
ADD REPLYlink written 3.0 years ago by Kevin Blighe71k

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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by bjwiley2320
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1666 users visited in the last hour
_