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===CSHL SNS caller=== *The method was developed by CSHL [http://www.nature.com/nprot/journal/v7/n6/full/nprot.2012.039.html Baslan et al. Nat Protoc, 2012]. *A Perl script [[Media:fastq2cnv.txt|fastq2cnv.pl]] was written to implement this method in both Triton and Genome-miner. *To run this script, one needs a .info file per sample. The file should contain the server name (the first line, either triton or genome-miner), location and other information of the sequencing data. Here is an [[Media:SAMPLE_NAME.info.txt|example]] of a .info file. *On genome-miner, the job can be started with the following command: nohup PATH_NAME/fastq2cnv.pl SAMPLE_NAME.info > SAMPLE_NAME_SNS.log & *On Triton, a job file needs to be created for each sample. And the job can be submitted by qsub. Here is an [[Media:SAMPLE_NAME.job.txt|example]] of .job file. qsub SAMPLE_NAME.job *Once the job is completed, transfer the SAMPLE_NAME.varbin50k.out to your local computer (you can also run R in genome-miner, but not triton). *Edit two R scripts by replacing the sample name with the actual one you are using. [[Media:SAMPLE_NAME.cbs.r.txt|SAMPLE_NAME.cbs.r]] [[Media:SAMPLE_NAME.copynumber.r.txt|SAMPLE_NAME.copynumber.r]] *Under R, run the following two commands (make sure both the varbin50k.out file and the R scripts are in the current directory). source("SAMPLE_NAME.cbs.r"); source("SAMPLE_NAME.copynumber.r"); *You will find two dozens of plots in the Postscript format, plus a number of other text files. Postscript files can be converted into pdf files using Acrobat Distiller, or ps2pdf in Unix/Linux. SAMPLE_NAME.hg19.50k.k50.varbin.data.copynumber. SAMPLE_NAME.hg19.50k.k50.nobad.varbin.data SAMPLE_NAME.hg19.50k.k50.nobad.varbin.short SAMPLE_NAME.hg19.50k.k50.varbin.data SAMPLE_NAME.hg19.50k.k50.varbin.short
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