Arichard:Computational/email from jeff
Hi Chris,
You can look in /home/jgole/JG_Ext12T/HL158. There you will find individual folders for each library. If you go in each folder, you can find the info files, which point to the fastq files in seqstore. You can also look at the status files to see what they should look like. You can try copying the info files to your own folder (or make your own info files). You will also see in the main folder (/home/jgole/JG_Ext12T/HL158) there are 4 scripts. You should copy fastqtoCNV and callCNVs each time. The mapData.sh is the shell script that I was talking about yesterday. It switches folders for each data set then runs fastq2cnv.pl. The getCNVdata.sh is a shell script that runs the binning python algorithm in callCNVs.sh. After running this script, you should go into the cbs folder generated for each library, and download the *.hg19.50k.k50.nobad.varbin.data.txt files for use in the Matlab scripts. The first 4 columns are what you need.
Jeff
On Thu, Aug 29, 2013 at 2:10 PM, Chris Wei <chriswei5262@gmail.com> wrote: Hey Jeff, I was wondering if you could send us the path to one of the datasets when genome miner is up, so we can practice this weekend? Thank you for going over the analysis with us today! I'll see you guys next Tuesday! Chris