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==CNV calling on single-cell genome sequencing data== ===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 ===BIC-Seq=== *This method was developed by Peter Park's group at Harvard. [http://www.pnas.org/content/108/46/E1128.short Xi et al. PNAS 2011] *It starts with mapped bam files after removal of clonal reads. *Step 1: generate read count files from the bam file (<b>replace DIR with a directory name to write all the .seq files</b>). /home/kunzhang/softwares/BICseq/PERL/BICseq_1.1.2/SAMgetUnique/samtools-0.1.7a_getUnique-0.1.1 view -U BWA,DIR/,N,N SAMPLE_NAME.bam Repeat the same procedure for each bam files, use one output directory per sample *Step 2: create a tab-delimited config file as the following: chrom case control chr1 case/chr1.seq control/chr1.seq chr2 case/chr2.seq control/chr2.seq *Step 3: run BIC-seq.pl: /home/kunzhang/softwares/BICseq/PERL/BICseq_1.1.2/BIC-seq/BIC-seq.pl [options] <ConfigFile> <OutputDir> <Description> Options: --help --lambda=<float>: default 2 --bin_size=<int>: default 100 --multiplicity=<float>: default 2 --window=<int>: the window for removing the outliers; default 200 --f=<float>: expected number of type I errors in the merging process; An alternative way to specify lambda --B=<int>: number of permutations for FDR estimate; default 0 --paired: if specified the data is treated as paired-end data --I=<Insert,SDofInsert>: specify the insert size and standard deviation of insert size. Default <200,20> <Outputdir>: the name of the directory to write the output (this cannot be an existing directory). <Description>: used to name the segmentation results under <OutputDir> *For detail, see /home/kunzhang/softwares/BICseq/PERL/BICseq_1.1.2/BIC-seq/README
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