SNS: Difference between revisions
Jump to navigation
Jump to search
m (→BIC-Seq) |
|||
(3 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
==CNV calling on single-cell genome sequencing data== | ==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]. | *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. | *A Perl script [[Media:fastq2cnv.txt|fastq2cnv.pl]] was written to implement this method in both Triton and Genome-miner. | ||
Line 7: | Line 8: | ||
*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]] | ||
Line 20: | Line 21: | ||
SAMPLE_NAME.hg19.50k.k50.varbin.data | SAMPLE_NAME.hg19.50k.k50.varbin.data | ||
SAMPLE_NAME.hg19.50k.k50.varbin.short | 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 |
Latest revision as of 18:28, 19 September 2012
CNV calling on single-cell genome sequencing data[edit]
CSHL SNS caller[edit]
- 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
BIC-Seq[edit]
- This method was developed by Peter Park's group at Harvard. 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 (replace DIR with a directory name to write all the .seq files).
/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