AlleleSeq - Revision history

Public: /* Usage */

2014-02-13T21:29:51Z

Usage

← Older revision		Revision as of 21:29, 13 February 2014
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	BNDS:=hits.bed ## binding site file; if NA, put any filename as placeholder <br>		BNDS:=hits.bed ## binding site file; if NA, put any filename as placeholder <br>
	MAPS:=$(BASE)/personal_genome/%s_NA12878.map ## location of MAP files from vcf2diploid pre-processing <br>		MAPS:=$(BASE)/personal_genome/%s_NA12878.map ## location of MAP files from vcf2diploid pre-processing <br>
	~~GENOMES:=$(BASE) ## location of pat and mat genomes <br>~~
	FDR_SIMS:=5 ## reads cut-off for simulations <br>		FDR_SIMS:=5 ## reads cut-off for simulations <br>
	FDR_CUTOFF:=0.1 ## false discovery rate q-value cutoff <br>		FDR_CUTOFF:=0.1 ## false discovery rate q-value cutoff <br>

2014-02-03T05:52:10Z

Input

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	'''(c)''' SNV genotype file; tab-delimited file of a set of SNV locations for each of		'''(c)''' SNV genotype file; tab-delimited file of a set of SNV locations for each of
	the trio: father, mother and child. AlleleSeq expects this format~~, WITHOUT the header~~: <br>		the trio: father, mother and child. AlleleSeq expects this format: <br>
	~~chr pos ref Mat Pat Child Phase~~
	1 114116078 A TT TT TA MUTANT		1 114116078 A TT TT TA MUTANT
	1 114117743 G CG GG GG HOMO		1 114117743 G CG GG GG HOMO

2014-02-03T05:51:35Z

Input

← Older revision		Revision as of 05:51, 3 February 2014
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	'''(c)''' SNV genotype file; tab-delimited file of a set of SNV locations for each of		'''(c)''' SNV genotype file; tab-delimited file of a set of SNV locations for each of
	the trio: father, mother and child. AlleleSeq expects this format, ~~with~~ the header: <br>		the trio: father, mother and child. AlleleSeq expects this format, WITHOUT the header: <br>
	chr pos ref Mat Pat Child Phase		chr pos ref Mat Pat Child Phase
	1 114116078 A TT TT TA MUTANT		1 114116078 A TT TT TA MUTANT

2014-02-03T05:33:29Z

Input

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	This can be generated from CNVnator (Abyzov et al. 2011).		This can be generated from CNVnator (Abyzov et al. 2011).
	A set of scripts has been provided [http://alleleseq.gersteinlab.org/tools.html here] to help with the conversion process. It is by no means the only way. <br><br>		A set of scripts has been provided [http://alleleseq.gersteinlab.org/tools.html here] to help with the conversion process using CNVnator. It is by no means the only way. <br><br>

	'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the		'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the

2014-02-03T05:32:56Z

Input

← Older revision		Revision as of 05:32, 3 February 2014
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	This can be generated from CNVnator (Abyzov et al. 2011).		This can be generated from CNVnator (Abyzov et al. 2011).
	A set of scripts has been provided ~~here to~~ [http://alleleseq.gersteinlab.org/~~alleleSeq_cnvScript~~.~~zip~~ help] with the conversion process. It is by no means the only way. <br><br>		A set of scripts has been provided [http://alleleseq.gersteinlab.org/tools.html here] to help with the conversion process. It is by no means the only way. <br><br>

	'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the		'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the

2014-02-03T05:32:03Z

Input

← Older revision		Revision as of 05:32, 3 February 2014
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	1 742429 0.976435		1 742429 0.976435

	This can be generated from CNVnator (Abyzov et al. 2011). <br><br>		This can be generated from CNVnator (Abyzov et al. 2011).
			A set of scripts has been provided here to [http://alleleseq.gersteinlab.org/alleleSeq_cnvScript.zip help] with the conversion process. It is by no means the only way. <br><br>

	'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the		'''(e)''' (optional) for ChIP-seq experiments, a set of "binding sites" for the

2013-10-22T01:42:31Z

Output

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	==Output==		==Output==
	(a) counts.txt: Contains count information for all heterozygous SNV locations. <br>		(a) counts.txt: Contains count information for all heterozygous SNV locations that have the minimum number of reads stipulated. <br>
	(b) counts.log: Contains information about why each SNV was judged significant. <br>		(b) counts.log: Contains information about why each SNV was judged significant. <br>
	(c) FDR.txt: the p-values and the corresponding q-values from the simulations <br>		(c) FDR.txt: the p-values and the corresponding q-values from the simulations <br>

2013-06-07T16:42:02Z

Output

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	(b) counts.log: Contains information about why each SNV was judged significant. <br>		(b) counts.log: Contains information about why each SNV was judged significant. <br>
	(c) FDR.txt: the p-values and the corresponding q-values from the simulations <br>		(c) FDR.txt: the p-values and the corresponding q-values from the simulations <br>
	(d) interestingHets.txt: This file contains information about all ~~SNP~~ locations		(d) interestingHets.txt: This file contains information about all SNV locations
	that passed all these tests: <br>		that passed all these tests: <br>
	- in a binding site <br>		- in a binding site <br>
	- within range for cnv test <br>		- within range for cnv test <br>
	- significantly assymetric by FDR test <br>		- significantly assymetric by FDR test <br>

2013-06-07T16:41:46Z

Output

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	==Output==		==Output==
	~~Main output Files:<br><br>~~
	(a) counts.txt: Contains count information for all heterozygous SNV locations. <br>		(a) counts.txt: Contains count information for all heterozygous SNV locations. <br>
	(b) counts.log: Contains information about why each SNV was judged significant. <br>		(b) counts.log: Contains information about why each SNV was judged significant. <br>

2013-06-07T16:41:33Z

Output

← Older revision		Revision as of 16:41, 7 June 2013
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	==Output==		==Output==
	Main output Files:		Main output Files:<br><br>
	(a) counts.txt: Contains count information for all heterozygous SNV locations.		(a) counts.txt: Contains count information for all heterozygous SNV locations. <br>
	(b) counts.log: Contains information about why each SNV was judged significant.		(b) counts.log: Contains information about why each SNV was judged significant. <br>
	(c) FDR.txt: the p-values and the corresponding q-values from the simulations		(c) FDR.txt: the p-values and the corresponding q-values from the simulations <br>
	(d) interestingHets.txt: This file contains information about all SNP locations		(d) interestingHets.txt: This file contains information about all SNP locations
	that passed all these tests:		that passed all these tests: <br>
	- in a binding site		- in a binding site <br>
	- within range for cnv test		- within range for cnv test <br>
	- significantly assymetric by FDR test		- significantly assymetric by FDR test <br>