GRAM - Revision history

Public: /* E. Pipeline */

2019-05-02T03:00:23Z

E. Pipeline

← Older revision		Revision as of 03:00, 2 May 2019
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	Sample report:		Sample report:
	GRAMMAR: parameter parsing done		GRAMMAR: parameter parsing done
	GRAMMAR: input variant bed file: ~~grammar.test/~~snptest.bed		GRAMMAR: input variant bed file: snptest.bed
	GRAMMAR: input gene expression file: ~~grammar.test/~~gexpr.test.bed		GRAMMAR: input gene expression file: gexpr.test.bed
	GRAMMAR: checking dependency done		GRAMMAR: checking dependency done
	GRAMMAR: checking genome fasta and gencode annotation configs done		GRAMMAR: checking genome fasta and gencode annotation configs done
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	==================================================		==================================================
	Step 2: Running GRAM predictor.		Step 2: Running GRAM predictor.
	GRAMMAR: cd /gram~~/GRAMMAR~~		GRAMMAR: cd gram
	GRAMMAR: Rscript gram~~/GRAMMAR~~/gram.predict.r grammar.test/ref.db.out ~~grammar.test/~~mut.db.out nc.var.bed ~~grammar.test/~~snp.4deepbind.bed ~~grammar.test/~~gexpr.test.bed ~~gram/~~GRAMMAR/model.rdata ~~grammar.test/~~snptest.bed.out/gram.score.txt<br>		GRAMMAR: Rscript gram/gram.predict.r grammar.test ref.db.out mut.db.out nc.var.bed snp.4deepbind.bed gexpr.test.bed GRAMMAR/model.rdata snptest.bed.out/gram.score.txt<br>
	[1] 20242 102		[1] 20242 102
	[1] "After filting, only 102 of 199 sample left for the prediction"<br>		[1] "After filting, only 102 of 199 sample left for the prediction"<br>
	GRAMMAR: Prediction results have been saved in ~~grammar.test/~~snptest.bed.out<br>		GRAMMAR: Prediction results have been saved in snptest.bed.out<br>
	--------------------------------------------------		--------------------------------------------------
	GRAMMAR: the prediction of GRAM score done		GRAMMAR: the prediction of GRAM score done
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	GRAMMAR: Results visualization done		GRAMMAR: Results visualization done
	==================================================		==================================================
	GRAMMAR: your job is done. please go to ~~/grammar.test/~~snptest.bed.out to find your results.		GRAMMAR: your job is done. please go to snptest.bed.out to find your results.
	==================================================		==================================================

Public: /* C. Configuration */

2019-05-02T02:57:15Z

C. Configuration

← Older revision		Revision as of 02:57, 2 May 2019
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	The pipeline grammar.sh should be configured prior to the first use. Please fill in the value of the below variables as instructed:		The pipeline grammar.sh should be configured prior to the first use. Please fill in the value of the below variables as instructed:

	genome: the path for genomic sequences (e.g. hg19.fa), the chromosome name is with "chr" prefix. You can download from UCSC ftp: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz		genome: the path for genomic sequences (e.g. hg19.fa), the chromosome name is with "chr" prefix. <br>
	gencode: the path for gencode annotation of cds regions (e.g. gencode.v19.cds.bed is available from GRAM github: https://github.com/gersteinlab/gram)		You can download from UCSC ftp: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz <br><br>
	dpath: the path for DeepBind model, there is a copy from GRAM github:https://github.com/gersteinlab/gram		gencode: the path for gencode annotation of cds regions (e.g. gencode.v19.cds.bed is available from GRAM github: https://github.com/gersteinlab/gram) <br><br>
			dpath: the path for DeepBind model, there is a copy from GRAM github:https://github.com/gersteinlab/gram <br><br>
	path_funseq: the path for FunSeq whole genome score file, which can be downloaded from funseq3.gersteinlab.org		path_funseq: the path for FunSeq whole genome score file, which can be downloaded from funseq3.gersteinlab.org

Public at 02:25, 2 May 2019

2019-05-02T02:25:50Z

← Older revision		Revision as of 02:25, 2 May 2019
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	~~_TOC__~~

	=Variant Prioritization=		=Variant Prioritization=

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	* [http://code.google.com/p/bedtools/downloads/list bedtools] (version bedtools-2.17.0) <br>		* [http://code.google.com/p/bedtools/downloads/list bedtools] (version bedtools-2.17.0) <br>
	* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>		* [http://sourceforge.net/projects/samtools/files/tabix/ tabix] (version tabix-0.2.6 and up) <br>
	* [http://www.r-project.org/ R] (require packages: andomForest, glmnet, reshape2, gplots) <br>		* [http://www.r-project.org/ R] (require packages: andomForest, glmnet, reshape2, gplots) <br>

	==B. Tool Download==		==B. Tool Download==

	This is a Linux/UNIX-based tool. At the command-line prompt, type the following.		This is a Linux/UNIX-based tool. At the command-line prompt, type the following.
	$ ~~tar xvf~~ gram.~~tar~~		$ git clone https://github.com/gersteinlab/gram.git

	==C. Configuration==		==C. Configuration==
	The pipeline grammar.sh should be configured prior to the first use. Please fill in the value of the below variables as instructed:		The pipeline grammar.sh should be configured prior to the first use. Please fill in the value of the below variables as instructed:

	genome: the path for genomic sequences (e.g. hg19.fa)		genome: the path for genomic sequences (e.g. hg19.fa), the chromosome name is with "chr" prefix. You can download from UCSC ftp: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz
	gencode: the path for gencode annotation of cds regions (e.g. gencode.v19.cds.bed)		gencode: the path for gencode annotation of cds regions (e.g. gencode.v19.cds.bed is available from GRAM github: https://github.com/gersteinlab/gram)
	dpath: the path for DeepBind model		dpath: the path for DeepBind model, there is a copy from GRAM github:https://github.com/gersteinlab/gram
	path_funseq: the path for FunSeq file		path_funseq: the path for FunSeq whole genome score file, which can be downloaded from funseq3.gersteinlab.org

	==D. Tool Usage==		==D. Tool Usage==
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	To display the usage of tool, type ‘./grammar.sh -h’. <br>		To display the usage of tool, type ‘./grammar.sh -h’. <br>
	* Usage : ./grammar~~.sh~~ -i bed -e exp ~~-d dpath -f fpath -o path~~		* Usage : ./grammar -i bed -e exp
	Options :<br>		Options :<br>
	-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)		-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)
	-e [Required] User Input gene expression matrix		-e [Required] User Input gene expression matrix
	~~-o [Required] Output path~~


	NOTE: Please make sure you have sufficient memory, at least 3G.		NOTE: Please make sure you have sufficient memory, at least 3G.

Public: /* D. Tool Usage */

2019-05-01T15:39:55Z

D. Tool Usage

← Older revision		Revision as of 15:39, 1 May 2019
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	To display the usage of tool, type ‘./grammar.sh -h’. <br>		To display the usage of tool, type ‘./grammar.sh -h’. <br>
	* Usage : ./grammar.sh -i bed -e exp -d dpath -f fpath -o path		* Usage : ./grammar.sh -i bed -e exp -d dpath -f fpath -o path
	Options :		Options :<br>
	-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)		-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)
	-e [Required] User Input gene expression matrix		-e [Required] User Input gene expression matrix

Public: /* D. Tool Usage */

2019-05-01T15:39:41Z

D. Tool Usage

← Older revision		Revision as of 15:39, 1 May 2019
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	* Usage : ./grammar.sh -i bed -e exp -d dpath -f fpath -o path		* Usage : ./grammar.sh -i bed -e exp -d dpath -f fpath -o path
	Options :		Options :
	-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)		-i [Required] User Input SNVs file (BED format: chr st ed ref mut sample-id rsid)
	-e [Required] User Input gene expression matrix		-e [Required] User Input gene expression matrix
	-o [Required] Output path		-o [Required] Output path


	NOTE: Please make sure you have sufficient memory, at least 3G.		NOTE: Please make sure you have sufficient memory, at least 3G.

	-i : Required format: chr st ed ref mut sample-id rsid<br>		-i : Required format: chr st ed ref mut sample-id rsid<br>

Public: /* E. Pipeline */

2019-05-01T15:36:02Z

E. Pipeline

← Older revision		Revision as of 15:36, 1 May 2019
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	Step 2: Running GRAM predictor.		Step 2: Running GRAM predictor.
	GRAMMAR: cd /gram/GRAMMAR		GRAMMAR: cd /gram/GRAMMAR
	GRAMMAR: Rscript gram/GRAMMAR/gram.predict.r grammar.test/ref.db.out grammar.test/mut.db.out nc.var.bed grammar.test/snp.4deepbind.bed grammar.test/gexpr.test.bed ~~/gpfs/slayman/pi/gerstein/from_louise/skltmp/tl/~~gram/GRAMMAR/model.rdata ~~/gpfs/ysm/home/tl444/Projects/GRAM/~~grammar.test/snptest.bed.out/gram.score.txt<br>		GRAMMAR: Rscript gram/GRAMMAR/gram.predict.r grammar.test/ref.db.out grammar.test/mut.db.out nc.var.bed grammar.test/snp.4deepbind.bed grammar.test/gexpr.test.bed gram/GRAMMAR/model.rdata grammar.test/snptest.bed.out/gram.score.txt<br>
	[1] 20242 102		[1] 20242 102
	[1] "After filting, only 102 of 199 sample left for the prediction"<br>		[1] "After filting, only 102 of 199 sample left for the prediction"<br>

Public: /* E. Pipeline */

2019-05-01T15:34:51Z

E. Pipeline

← Older revision		Revision as of 15:34, 1 May 2019
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	==E. Pipeline==		==E. Pipeline==

			The pipeline:
	[[File::http://funseq3.gersteinlab.org/GRAMMAR.pipeline.png]]		[[File::http://funseq3.gersteinlab.org/GRAMMAR.pipeline.png]]

Public: /* E. Tool Usage */

2019-05-01T15:34:26Z

E. Tool Usage

@@ Line 41: / Line 41: @@
 -e: The rows correspond to genes and columns correspond to samples. Sample ids need to match with those in the variant bed file. <br>
-==E. Tool Usage==
+==E. Pipeline==
 ==F. Input files==

Public: /* Variant Prioritization */

2019-05-01T15:06:44Z

Variant Prioritization

← Older revision		Revision as of 15:06, 1 May 2019
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	-e: The rows correspond to genes and columns correspond to samples. Sample ids need to match with those in the variant bed file. <br>		-e: The rows correspond to genes and columns correspond to samples. Sample ids need to match with those in the variant bed file. <br>

	==E. Input files==		==E. Tool Usage==

			==F. Input files==
	* User input SNV file (-i): BED format		* User input SNV file (-i): BED format

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	… … … … … …		… … … … … …

	==F. Output files==		==G. Output files==
	Five output files will be generated: ‘Output.format’, ‘Output.indel.format’, ‘Recur.Summary’, ‘Candidates.Summary’ and ‘Error.log’. Output.format: stores detailed results for all samples; Output.indel.format: contains results for indels; Recur.Summary: the recurrence result when having multiple samples; Candidates.Summary: brief output of potential candidates (coding nonsynonymous/prematurestop variants, non-coding variants with score (>= 5 of un-weighted scoring scheme and >=1.5 for weighted scoring scheme) and variants in or associated with known cancer genes); Error.log: error information. For un-weighted scoring scheme, each feature is given value 1.		Five output files will be generated: ‘Output.format’, ‘Output.indel.format’, ‘Recur.Summary’, ‘Candidates.Summary’ and ‘Error.log’. Output.format: stores detailed results for all samples; Output.indel.format: contains results for indels; Recur.Summary: the recurrence result when having multiple samples; Candidates.Summary: brief output of potential candidates (coding nonsynonymous/prematurestop variants, non-coding variants with score (>= 5 of un-weighted scoring scheme and >=1.5 for weighted scoring scheme) and variants in or associated with known cancer genes); Error.log: error information. For un-weighted scoring scheme, each feature is given value 1.

Public: /* E. Input files */

2019-05-01T15:03:50Z

E. Input files

← Older revision		Revision as of 15:03, 1 May 2019
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	* User input SNV file (-i): BED format		* User input SNV file (-i): BED format

	In addition to the three required BED fields, please prepare your files as following (5 required fields, tab delimited;		In addition to the three required BED fields, please prepare your files as following (5 required fields, tab delimited);
	the 6th column is reserved for sample names, do not put other information there):		the 6th column is reserved for sample names, do not put other information there):
	chromosome, start position, end position, reference allele, alternative allele, sample id, rsid.		chromosome, start position, end position, reference allele, alternative allele, sample id, rsid.
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	* User input expression matrix (-e)		* User input expression matrix (-e)
	The gene expression file should be prepared as a matrix with first column stores gene names (use gene symbols) and first row as sample names. Other fields are gene expression data either in RPKM or raw read counts format. Tab delimited.		The gene expression file should be prepared as a matrix with first column stores gene names (use gene symbols) and first row as sample names. Other fields are gene expression data either in RPKM or raw read counts format. Tab delimited.

	e.g.		e.g.
	Gene Sample1 Sample2 Sample3 Sample4 …		Gene Sample1 Sample2 Sample3 Sample4 …