Icbwiki - Recent changes [en]

GeneTools

2013-02-01T04:42:13Z

/* Extracting all exonic regions from the genome */

Revision as of 04:42, 1 February 2013		Current revision
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	== '''geneTools''' ==		== '''geneTools''' ==
-	GeneTools is developed by Dr. David Soong at the [[http://physiology.med.cornell.edu/faculty/elemento/lab/ Elemento lab]]. Please contact us at genetools.cornell@gmail.com if you have questions or would like to use our software.	+	GeneTools is developed by Dr. David Soong at the [[http://physiology.med.cornell.edu/faculty/elemento/lab/ Elemento lab]]. Please contact us at genetools.cornell@gmail.com if you have questions, suggestions, or would like to use our software.

	<span style="color:#FF0000">'''IMPORTANT: If you need a copy of the software, please use "GeneTools software request" in the subject line when emailing us. Thank you.'''</span>		<span style="color:#FF0000">'''IMPORTANT: If you need a copy of the software, please use "GeneTools software request" in the subject line when emailing us. Thank you.'''</span>
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	==NGS Pipeline==		==NGS Pipeline==
-	This program generates scripts for pre-processing reads, performing QC analysis, doing sequence alignment (TopHat, BWA), visualization, etc.	+	This program generates [http://en.wikipedia.org/wiki/Oracle_Grid_Engine Sun Grid Engine] scripts for pre-processing reads, performing QC analysis, doing sequence alignment (TopHat, BWA), visualization, etc.
	scripts/pipelineSeq.pl		scripts/pipelineSeq.pl

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	==SNV related==		==SNV related==
	===Detect SNVs from a BAM file===		===Detect SNVs from a BAM file===
-	* Call the SNVs from a sorted BAM file. This will also generate an SNV output file in [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNVseeqer_Tutorial SNVseeqer] format (output_SNVsqr.txt)	+	* Call the SNVs from a sorted BAM file. This will also generate an SNV output file in [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNVseeqer_Tutorial SNVseeqer] format (output_SNVsqr.txt). Our method of SNV detection is described in our [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0040332 PLoS One paper]
	./geneModel bam -cmd snv -i alignment/accepted_hits.bam -f ~/databases/hg18.fa --uniq -o SNVs.txt		./geneModel bam -cmd snv -i alignment/accepted_hits.bam -f ~/databases/hg18.fa --uniq -o SNVs.txt
	'''Options:'''		'''Options:'''
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	NOTE: The (non-overlapping) exon regions will be in ChIP-seq format.		NOTE: The (non-overlapping) exon regions will be in ChIP-seq format.
		+
		+	===Generate gene coordinates in interval format===
		+	This function can be used to generate gene body regions, promotor regions (e.g. TSS +/- 2kb), gene ends, or gene neighborhoods (e.g. TSS- 10kb ~ TES+10kb).
		+
		+	./gmm dna -cmd ranges -o data/all_gene_ranges_50kb.txt
		+	'''Options:'''
		+	-i Input file containing a list of genes
		+	-ref RefSeq definition file
		+	-ext extend genes by n bp up of TSS and downstream of TES
		+	--TSS Output coordinates around the TSS only. (--TSS trumps --TES)
		+	--TES Output coordinates around the TES only
		+	--pair Output in paired-block format
		+	--strand Output additional column containing the strand
		+	-o Output file

	===Get gene transcript structure===		===Get gene transcript structure===

GeneTools FAQ

2013-02-01T04:19:17Z

/* FAQ */

New page

== FAQ ==
* I got the following error message when running genetools, what should I do?
error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory

Ans:
The program requires the PCRE library (Perl Compatible Regular Expressions). Please download from [http://www.pcre.org/ http://www.pcre.org/] and install it. The version we use is 8.02.

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

GeneTools

2013-02-01T04:11:39Z

/* Related pages */

Revision as of 04:11, 1 February 2013		Current revision
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	* [http://icb.med.cornell.edu/wiki/index.php/GeneTools_Indel GeneTools Indel]		* [http://icb.med.cornell.edu/wiki/index.php/GeneTools_Indel GeneTools Indel]
	* [http://icb.med.cornell.edu/wiki/index.php/GeneTools_DINDEL GeneTools DINDEL]		* [http://icb.med.cornell.edu/wiki/index.php/GeneTools_DINDEL GeneTools DINDEL]
		+	* [http://icb.med.cornell.edu/wiki/index.php/GeneTools_FAQ GeneTools FAQ]

	==NGS Pipeline==		==NGS Pipeline==

GeneTools installation

2013-01-31T03:14:07Z

Revision as of 03:14, 31 January 2013		Current revision
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		+	'''Read this first'''
		+	* The SVN repository is currently open only to internal users. But [http://icb.med.cornell.edu/wiki/index.php/GeneTools#geneTools we have a precompiled version of GeneTools]. Please email us to request a copy of the software.
		+
	'''Requirements'''		'''Requirements'''
	* GNU C++ compiler		* GNU C++ compiler

GeneTools

2013-01-31T03:07:03Z

/* '''geneTools''' */

Revision as of 03:07, 31 January 2013		Current revision
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	== '''geneTools''' ==		== '''geneTools''' ==
	GeneTools is developed by Dr. David Soong at the [[http://physiology.med.cornell.edu/faculty/elemento/lab/ Elemento lab]]. Please contact us at genetools.cornell@gmail.com if you have questions or would like to use our software.		GeneTools is developed by Dr. David Soong at the [[http://physiology.med.cornell.edu/faculty/elemento/lab/ Elemento lab]]. Please contact us at genetools.cornell@gmail.com if you have questions or would like to use our software.
		+
		+	<span style="color:#FF0000">'''IMPORTANT: If you need a copy of the software, please use "GeneTools software request" in the subject line when emailing us. Thank you.'''</span>

	==Related pages==		==Related pages==

Elementolab/Cancer Exome Mutation Discovery pipeline

2013-01-30T22:30:00Z

/* LOH analysis */

Revision as of 22:30, 30 January 2013		Current revision
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	Visualize the LOH map:		Visualize the LOH map:
	/opt/local/bin/perl5.16 ~/PROGRAMS/SNPseeqer/SCRIPTS/DrawLOHmapImproved.pl --snvdata=table.txt --chrdata=/$HOME/PROGRAMS/SNPseeqer/REFDATA/hg19.chrdata		/opt/local/bin/perl5.16 ~/PROGRAMS/SNPseeqer/SCRIPTS/DrawLOHmapImproved.pl --snvdata=table.txt --chrdata=/$HOME/PROGRAMS/SNPseeqer/REFDATA/hg19.chrdata
		+
		+	Options
		+	--tumorlabel=R1 --normallabel=D # change the tumor/normal labels

Elementolab/

2013-01-30T21:53:46Z

Revision as of 21:53, 30 January 2013		Current revision
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	* '''Resources'''		* '''Resources'''
		+	** [https://sites.google.com/site/epiworkshop2013/ Epiworkshop 2013]
	** [https://sites.google.com/site/epiworkshop2012/ Epiworkshop 2012]		** [https://sites.google.com/site/epiworkshop2012/ Epiworkshop 2012]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/CSHL Elemento lab participation in CSHL Summer School]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/CSHL Elemento lab participation in CSHL Summer School]

Elementolab/Cancer Exome Mutation Discovery pipeline

2013-01-30T00:04:25Z

/* Alignment */

Revision as of 00:04, 30 January 2013		Current revision
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		+	=Alignment=
		+
		+	We use BWA with default parameters for alignment.
		+
		+	For single-end reads
		+	perl ~/PROGRAMS/SNPseeqer/SCRIPTS/PBS_quickAlign.pl --fastq=s_1_sequence.txt.gz --bwaidx=/pbtech_mounts/oelab_scratch002/ole2001/DATA/GENOMES/hg19/hg19bwaidx --submit=1
		+
		+	For paired-end
		+	perl ~/PROGRAMS/SNPseeqer/SCRIPTS/PBS_quickAlignPE.pl --fastq1=s_1_1_sequence.txt.gz --fastq1=s_1_2_sequence.txt.gz \
		+	--bwaidx=/pbtech_mounts/oelab_scratch002/ole2001/DATA/GENOMES/hg19/hg19bwaidx --submit=1
		+
		+	(use --submit=0 to see the PBS script without submitting)

	=SNV analysis=		=SNV analysis=

Elementolab/BWA tutorial

2013-01-27T01:42:31Z

/* Mapping short reads to the reference genome, eg hg19 */

Revision as of 01:42, 27 January 2013		Current revision
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	bwa samse hg19bwaidx s_3_sequence.txt.bwa s_3_sequence.txt.gz > s_3_sequence.txt.sam		bwa samse hg19bwaidx s_3_sequence.txt.bwa s_3_sequence.txt.gz > s_3_sequence.txt.sam

-	Note:	+	Note 1:
	BWA is capable of aligning reads stored in the compressed format (*.gz). You can gzip your reads to save disk space.		BWA is capable of aligning reads stored in the compressed format (*.gz). You can gzip your reads to save disk space.
		+
		+	Note 2: for paired end reads, you need to align each end (R1 and R2) separarely:
		+
		+	bwa aln -t 4 hg19bwaidx s_3_1_sequence.txt.gz > s_3_1_sequence.txt.bwa
		+	bwa aln -t 4 hg19bwaidx s_3_2_sequence.txt.gz > s_3_2_sequence.txt.bwa
		+	bwa sampe hg19bwaidx s_3_1_sequence.txt.bwa s_3_2_sequence.txt.bwa s_3_1_sequence.txt.gz s_3_2_sequence.txt.gz > s_3_sequence.txt.sam
		+
		+	Typically, after this step, you can split the reads using our split_samfile tool, or convert SAM to BAM

	===Mapping short reads to RefSeq mRNAs===		===Mapping short reads to RefSeq mRNAs===