Funseq - Revision history

Public: /* Input */

2013-10-17T21:42:06Z

Input

← Older revision		Revision as of 21:42, 17 October 2013
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	:# chrom - The name of the chromosome (e.g. chr3, chrY). <br>		:# chrom - The name of the chromosome (e.g. chr3, chrY). <br>
	:# chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.		:# chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
	:# chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:# chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature. <br>For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
	::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		:# Reference.allele - The reference allele of SNVs
	:## Reference.allele - The reference allele of SNVs		:# Alternative.allele - The alternative allele of SNVs.
	:## Alternative.allele - The alternative allele of SNVs.

	2. VCF format (http://www.1000genomes.org/node/101) <br>		2. VCF format (http://www.1000genomes.org/node/101) <br>

Public: /* Input */

2013-10-17T21:41:51Z

Input

← Older revision		Revision as of 21:41, 17 October 2013
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	:# chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:# chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.
	::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
	:# Reference.allele - The reference allele of SNVs		:## Reference.allele - The reference allele of SNVs
	:# Alternative.allele - The alternative allele of SNVs.		:## Alternative.allele - The alternative allele of SNVs.

	2. VCF format (http://www.1000genomes.org/node/101) <br>		2. VCF format (http://www.1000genomes.org/node/101) <br>

Public: /* Input */

2013-10-17T21:41:40Z

Input

← Older revision		Revision as of 21:41, 17 October 2013
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	:# chrom - The name of the chromosome (e.g. chr3, chrY). <br>		:# chrom - The name of the chromosome (e.g. chr3, chrY). <br>
	:# chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.		:# chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
	:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:# chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.
	::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
	:* Reference.allele - The reference allele of SNVs		:# Reference.allele - The reference allele of SNVs
	:* Alternative.allele - The alternative allele of SNVs.		:# Alternative.allele - The alternative allele of SNVs.

	2. VCF format (http://www.1000genomes.org/node/101) <br>		2. VCF format (http://www.1000genomes.org/node/101) <br>

Public: /* Input */

2013-10-17T21:41:30Z

Input

← Older revision		Revision as of 21:41, 17 October 2013
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	In addition to the three required BED fields, please prepare your file as follows (5 required fields, tab-delimited): <br>		In addition to the three required BED fields, please prepare your file as follows (5 required fields, tab-delimited): <br>
	chrom chromStart chromEnd Reference.allele Alterative.allele ... <br>		chrom chromStart chromEnd Reference.allele Alterative.allele ... <br>
	:* chrom - The name of the chromosome (e.g. chr3, chrY). <br>		:# chrom - The name of the chromosome (e.g. chr3, chrY). <br>
	:* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.		:# chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
	:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.
	::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

Public: /* Input */

2013-10-17T21:41:04Z

Input

← Older revision		Revision as of 21:41, 17 October 2013
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	:* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.		:* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
	:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.
	:For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		::For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
	:* Reference.allele - The reference allele of SNVs		:* Reference.allele - The reference allele of SNVs
	:* Alternative.allele - The alternative allele of SNVs.		:* Alternative.allele - The alternative allele of SNVs.

Public: /* Input */

2013-10-17T21:40:52Z

Input

← Older revision		Revision as of 21:40, 17 October 2013
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	In addition to the three required BED fields, please prepare your file as follows (5 required fields, tab-delimited): <br>		In addition to the three required BED fields, please prepare your file as follows (5 required fields, tab-delimited): <br>
	chrom chromStart chromEnd Reference.allele Alterative.allele ... <br>		chrom chromStart chromEnd Reference.allele Alterative.allele ... <br>
	* chrom - The name of the chromosome (e.g. chr3, chrY). <br>		:* chrom - The name of the chromosome (e.g. chr3, chrY). <br>
	* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.		:* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
	* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.		:* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature.
	For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.		:For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
	* Reference.allele - The reference allele of SNVs		:* Reference.allele - The reference allele of SNVs
	* Alternative.allele - The alternative allele of SNVs.		:* Alternative.allele - The alternative allele of SNVs.

	2. VCF format (http://www.1000genomes.org/node/101) <br>		2. VCF format (http://www.1000genomes.org/node/101) <br>

Public: /* Usage */

2013-10-17T21:40:27Z

Usage

← Older revision		Revision as of 21:40, 17 October 2013
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	*'' Usage: ./funseq –f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file -cls file -exf <rpkm/raw>''		*'' Usage: ./funseq –f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file -cls file -exf <rpkm/raw>''
	:''Options : '' <br>		:''Options : '' <br>
	~~<nowiki>~~
	-f User Input SNVs File <br>		-f User Input SNVs File <br>
	-maf Minor Allele Frequency Threshold to filter 1KG SNVs		-maf Minor Allele Frequency Threshold to filter 1KG SNVs
	-m 1 - Somatic Genome; 2 - Germline or Personal Genome		-m 1 - Somatic Genome; 2 - Germline or Personal Genome
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	-cls [Optional] class file for samples in gene expression matrix		-cls [Optional] class file for samples in gene expression matrix
	-exf [Optional] gene expression format - rpkm / raw		-exf [Optional] gene expression format - rpkm / raw
	~~</nowiki>~~
	:''Default Options: -maf 0 -m 1 -outf vcf -o out''		:''Default Options: -maf 0 -m 1 -outf vcf -o out''

Public: /* Usage */

2013-10-17T21:39:29Z

Usage

← Older revision		Revision as of 21:39, 17 October 2013
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	:''Options : '' <br>		:''Options : '' <br>
	<nowiki>		<nowiki>
	-f User Input SNVs File		-f User Input SNVs File <br>
	-maf Minor Allele Frequency Threshold to filter 1KG SNVs		-maf Minor Allele Frequency Threshold to filter 1KG SNVs
	-m 1 - Somatic Genome; 2 - Germline or Personal Genome		-m 1 - Somatic Genome; 2 - Germline or Personal Genome

Public: /* Usage */

2013-10-17T21:39:15Z

Usage

← Older revision		Revision as of 21:39, 17 October 2013
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	*'' Usage: ./funseq –f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file -cls file -exf <rpkm/raw>''		*'' Usage: ./funseq –f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file -cls file -exf <rpkm/raw>''
	:''Options : '' <br>		:''Options : '' <br>
	<~~center~~>		<nowiki>
	-f User Input SNVs File		-f User Input SNVs File
	-maf Minor Allele Frequency Threshold to filter 1KG SNVs		-maf Minor Allele Frequency Threshold to filter 1KG SNVs
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	-cls [Optional] class file for samples in gene expression matrix		-cls [Optional] class file for samples in gene expression matrix
	-exf [Optional] gene expression format - rpkm / raw		-exf [Optional] gene expression format - rpkm / raw
	</~~center~~>		</nowiki>
	:''Default Options: -maf 0 -m 1 -outf vcf -o out''		:''Default Options: -maf 0 -m 1 -outf vcf -o out''

Public: /* Usage */

2013-10-17T21:37:51Z

Usage

← Older revision		Revision as of 21:37, 17 October 2013
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	:''Options : '' <br>		:''Options : '' <br>
	<center>		<center>
	-f User Input SNVs File		-f User Input SNVs File
	-maf Minor Allele Frequency Threshold to filter 1KG SNVs		-maf Minor Allele Frequency Threshold to filter 1KG SNVs
	-m 1 - Somatic Genome; 2 - Germline or Personal Genome		-m 1 - Somatic Genome; 2 - Germline or Personal Genome