SNS

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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.
  • 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