GREGOR - Revision history

Jchen: /* Download reference files */

2016-11-15T21:39:09Z

Download reference files

← Older revision		Revision as of 17:39, 15 November 2016
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	ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].		ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].

	Reference files is created ~~by populations~~(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).		Reference files are created for the different population groups(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).

	If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.		If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.

Jchen: /* Configuration File */

2016-11-15T21:38:12Z

Configuration File

← Older revision		Revision as of 17:38, 15 November 2016
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	###############################################################################		###############################################################################
	BATCHTYPE = local ## run jobs on local machine		BATCHTYPE = local ## run jobs on local machine
	~~BATCHTYPE = slurm~~
	~~BATCHOPTS = --partition=main --time=0:30:0~~

	In the config file, there are several parameters to adjust:		In the config file, there are several parameters to adjust:

Jchen: /* GREGOR */

2016-11-15T21:24:38Z

GREGOR

← Older revision		Revision as of 17:24, 15 November 2016
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	==GREGOR==		==GREGOR==

	'''GREGOR''' ('''~~_G_~~'''enomic '''_R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.		'''GREGOR''' ('''G'''enomic '''R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.

	Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.		Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.

Jchen: /* GREGOR */

2016-11-15T21:23:12Z

GREGOR

← Older revision		Revision as of 17:23, 15 November 2016
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	==GREGOR==		==GREGOR==

	'''GREGOR''' ('''_G'''enomic '''_R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.		'''GREGOR''' ('''_G_'''enomic '''_R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.

	Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.		Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.

Jchen: /* GREGOR */

2016-11-15T21:22:59Z

GREGOR

← Older revision		Revision as of 17:22, 15 November 2016
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	==GREGOR==		==GREGOR==

	'''GREGOR''' ('''G'''enomic '''R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.		'''GREGOR''' ('''_G'''enomic '''_R'''egulatory '''E'''lements and '''G'''was '''O'''verlap algo'''R'''ithm) is a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.

	Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.		Because all reference data are version hg19, please make sure that your index SNP list and BED files are also version hg19.

Jchen: /* Configuration File */

2016-11-15T21:21:32Z

Configuration File

← Older revision		Revision as of 17:21, 15 November 2016
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	REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".		REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".

	R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 ≥ 0.7		R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 ≥ 0.7， you can define this number between 1 and 0.7.

	OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".		OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
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	BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.		BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.

	~~BATCHTYPE~~: We have ~~three options for this parameter~~. When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".		POPULATION: If you use reference file "AFR", define this to AFR. You have 5 optiones: AFR, AMR, ASN, EUR and SAN.

			GREGOR can run on local machine or on the cluster with MOSIX or SLURM.
			BATCHTYPE: When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".

	BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"		BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"

Jchen: /* Configuration File */

2016-11-15T21:17:42Z

Configuration File

← Older revision		Revision as of 17:17, 15 November 2016
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	REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".		REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".

	R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 &le 0.7		R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 ≥ 0.7

	OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".		OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".

Jchen: /* Configuration File */

2016-11-15T21:16:23Z

Configuration File

← Older revision		Revision as of 17:16, 15 November 2016
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	R2THRESHOLD = 0.7		R2THRESHOLD = 0.7
	LDWINDOWSIZE = 1000000		LDWINDOWSIZE = 1000000
	OUT_DIR = ~~/workingdirectory/example/example.rsid.20130808/ ## e.g.~~ /workingdirectory/example/example.rsid.20130808/		OUT_DIR = /workingdirectory/example/example.rsid.20130808/
	MIN_NEIGHBOR_NUM = 500		MIN_NEIGHBOR_NUM = 500
	BEDFILE_IS_SORTED = True		BEDFILE_IS_SORTED = True
			POPULATION = AFR ## define the population, you can specify EUR, AFR, AMR or ASN
			TOPNBEDFILES = 2
			JOBNUMBER = 10
			###############################################################################
			#BATCHTYPE = mosix ## submit jobs on MOSIX
			#BATCHOPTS = -E/tmp -i -m2000 -j10,11,12,13,14,15,16,17,18,19,120,122,123,124,125 sh -c
			###############################################################################
			#BATCHTYPE = slurm ## submit jobs on SLURM
			#BATCHOPTS = --partition=main --time=0:30:0
			###############################################################################
			BATCHTYPE = local ## run jobs on local machine
	BATCHTYPE = slurm		BATCHTYPE = slurm
	BATCHOPTS = --partition=main --time=0:30:0		BATCHOPTS = --partition=main --time=0:30:0
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	BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.		BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.

	REF_DIR: Define reference file directory which you download at here.		REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".

	R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size.		R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 &le 0.7

	OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".		OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".

Jchen: /* Configuration File */

2016-11-15T21:10:48Z

Configuration File

← Older revision		Revision as of 17:10, 15 November 2016
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	## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY		## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
	###############################################################################		###############################################################################
	INDEX_SNP_FILE = ~~/workingdirectory/example/example.index.snps.rsid.list.txt ## e.g.~~ /workingdirectory/example/example.index.snps.rsid.list.txt		INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt
	BED_FILE_INDEX = ~~/workingdirectory/example/example.bed.file.index ## e.g.~~ /workingdirectory/example/example.bed.file.index		BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index
	REF_DIR = /workingdirectory/ref/ ~~## reference directory~~		REF_DIR = /workingdirectory/ref/
	R2THRESHOLD = 0.7		R2THRESHOLD = 0.7
	LDWINDOWSIZE = 1000000		LDWINDOWSIZE = 1000000

Jchen: /* Download reference files */

2016-11-15T21:08:26Z

Download reference files

← Older revision		Revision as of 17:08, 15 November 2016
Line 21:		Line 21:
	ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].		ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].

	Reference files is created by populations(AFR, AMR, ASN, EUR, SAN) from 1000G data.		Reference files is created by populations(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).

	If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.		If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.