Icbwiki - Recent changes [en]

Elementolab/Cancer Exome Mutation Discovery pipeline

2013-04-22T19:15:47Z

Revision as of 19:15, 22 April 2013		Current revision
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	scp -r -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com:/home/ec2-user/portal-data/studies/		scp -r -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com:/home/ec2-user/portal-data/studies/
		+

	Login and load data		Login and load data

2013-04-18T16:27:57Z

/* Print the content of a binary wiggle file */

Revision as of 16:27, 18 April 2013		Current revision
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	-o Output binary Wiggle file		-o Output binary Wiggle file
	-res Resolution (bin size)		-res Resolution (bin size)
		+	--norm Normalize by resolution (i.e. calculate average read count instead of total read count)
		+	--peak Treat each record as a peak (i.e. ignore column 4 and add count 1)

	===Print the content of a binary wiggle file===		===Print the content of a binary wiggle file===
	./geneModel chip -cmd print-bin-wig [options]		./geneModel chip -cmd print-bin-wig [options]
	-i Binary wiggle file		-i Binary wiggle file
		+	--interval Print in ChIP-seq interval format (by default is off, i.e. shows in the internal format)
		+	--avg Show average read count instead of total read count (i.e. normalize by bin size)
		+	--smooth
		+	-k
		+	--nonzero If specified, print only the non-zero entries

	===Extend the peak intervals by n-bp on each side===		===Extend the peak intervals by n-bp on each side===

2013-04-18T15:35:46Z

Revision as of 15:35, 18 April 2013		Current revision
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	* Which genomes does geneTools support?		* Which genomes does geneTools support?
	Ans:		Ans:
-	Currently we only support the human genome (hg18 and hg19) but are working on incorporating additional ones. Please let us know if there are genomes you'd like us to support.	+	Currently we only support the human genome (hg18 and hg19) but are working on incorporating additional ones. An experimental version supports mouse (mm9, mm10), drosophila (dm3), and C. elegans (ce6, ce10). Please let us know if there are genomes you'd like us to support.

	== Related pages ==		== Related pages ==
	* [[GeneTools]]		* [[GeneTools]]
	* [[GeneTools installation]]		* [[GeneTools installation]]

2013-04-15T00:29:49Z

Revision as of 00:29, 15 April 2013		Current revision
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	CNA.object <-CNA( genomdat = log2(cn[,8]), chrom = cn[,1], maploc = cn[,2]+(cn[,3]-cn[,2])/2, data.type = 'logratio', sampleid="DLBCL patient")		CNA.object <-CNA( genomdat = log2(cn[,8]), chrom = cn[,1], maploc = cn[,2]+(cn[,3]-cn[,2])/2, data.type = 'logratio', sampleid="DLBCL patient")
	CNA.smoothed <- smooth.CNA(CNA.object)		CNA.smoothed <- smooth.CNA(CNA.object)
-	segs <- segment(CNA.smoothed, undo.splits = "sdundo", undo.SD = 3, verbose = 1)	+	segs <- segment(CNA.smoothed, undo.splits = "sdundo", undo.SD = 1.5, verbose = 1, min.width=5)
		+
	plot(segs, plot.type="s", ylim=c(-2,2))		plot(segs, plot.type="s", ylim=c(-2,2))
	write.table(segs$output, file="segments.txt", row.names=F, col.names=F, quote=F, sep="\t")		write.table(segs$output, file="segments.txt", row.names=F, col.names=F, quote=F, sep="\t")
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	sudo /etc/init.d/tomcat6 stop		sudo /etc/init.d/tomcat6 stop
	sudo /etc/init.d/tomcat6 start		sudo /etc/init.d/tomcat6 start
		+
		+
		+	The cBio portal does not support incremental updates; therefore if you want to add new patients to an existing study, you \
		+	need to delete the database, and reload the updated one from scratch
		+
		+	mysql -u root -p
		+	[enter without password]
		+	drop database cgds_public
		+	create database cgds_public
		+	exit
		+
		+	Then:
		+
		+	initdb
		+	importreferencedata
		+	# import your dataset using the commands above
		+	...
		+	deployportal

2013-04-01T14:46:59Z

/* Extracting all exonic regions from the genome */

Revision as of 14:46, 1 April 2013		Current revision
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	==Gene related==		==Gene related==
	===Extracting all exonic regions from the genome===		===Extracting all exonic regions from the genome===
-	./geneModel dna -ref refGene.txt -o refGene_exons.txt	+	./geneModel dna -cmd exons -ref refGene.txt -o refGene_exons.txt
	'''Options:'''		'''Options:'''
	-ref RefSeq definition file		-ref RefSeq definition file
	-o Output file		-o Output file
		+	--merge Merge overlapping exons
		+	--full Output transcript name + exon id

	NOTE: The (non-overlapping) exon regions will be in ChIP-seq format.		NOTE: The (non-overlapping) exon regions will be in ChIP-seq format.