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*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. | *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 | qsub SAMPLE_NAME.job | ||
*Once the job is completed, transfer the SAMPLE_NAME.varbin50k.out to your local computer. | *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. | *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.cbs.r.txt|SAMPLE_NAME.cbs.r]] |
Revision as of 20:58, 2 August 2012
CNV calling on single-cell genome sequencing data
- The method was developed by CSHL Baslan et al. Nat Protoc, 2012.
- A Perl script 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 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 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.
SAMPLE_NAME.cbs.r 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