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Elementolab/SNPseeqer Install

Ole2001 — Tue, 24 Nov 2009 22:25:20 GMT

Revision as of 22:25, 24 November 2009		Current revision
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	cat *.fa > wg.fa		cat *.fa > wg.fa
	export HG18DIR=`pwd`		export HG18DIR=`pwd`
		+
		+	* dbSNP release 130
		+	cd REFDATA
		+

	You are now ready to use SNPseeqer. Please take a look at the [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Tutorial tutorial] for more information on how to use the program.		You are now ready to use SNPseeqer. Please take a look at the [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Tutorial tutorial] for more information on how to use the program.

Elementolab/ChIPseeqer Summary

Ole2001 — Tue, 24 Nov 2009 21:23:42 GMT

Revision as of 21:23, 24 November 2009		Current revision
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	2. Type the command:		2. Type the command:

-	$ ./ChIPseeqerSummary --targets='''TF_targets.txt''' --lenu='''1000''' -lend='''500''' --prefix='''TF_targets_SUM'''	+	$ ./ChIPseeqerSummary --targets='''TF_targets.txt''' --lenu='''2000''' -lend='''500''' --prefix='''TF_targets_SUM'''

	The following options are available:		The following options are available:

Elementolab/Perl Tips

Ole2001 — Mon, 23 Nov 2009 20:38:36 GMT

Revision as of 20:38, 23 November 2009		Current revision
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	* A nice Perl module to create Excel spreadsheets in Perl: Spreadsheet::WriteExcel		* A nice Perl module to create Excel spreadsheets in Perl: Spreadsheet::WriteExcel
		+
		+	http://homepage.eircom.net/~jmcnamara/perl/WriteExcel.html
		+	http://search.cpan.org/dist/Spreadsheet-WriteExcel/

	* Connected components (using Olivier's Sets.pm multipurpose module)		* Connected components (using Olivier's Sets.pm multipurpose module)

Elementolab/Deep Sequencing Resources

Ole2001 — Sun, 22 Nov 2009 19:46:28 GMT

Revision as of 19:46, 22 November 2009		Current revision
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	* BWA http://bio-bwa.sourceforge.net/bwa.shtml		* BWA http://bio-bwa.sourceforge.net/bwa.shtml

-	To create the index using one of the direwulf fat nodes (using Olivier's GR tools):	+	To create the index:
-	gr_1n_fat "bwa index -p hg18bwaidx -a bwtsw wg.fa " bwaindex	+	bwa index -p hg18bwaidx -a bwtsw wg.fa
		+
		+	To align (using 4 threads):
		+	bwa aln -t 4 hg18bwaidx s_3_sequence.txt > s_3_sequence.txt.bwa
		+
		+	To create alignment in the SAM format:
		+
		+	bwa samse hg18bwaidx s_3_sequence.txt.bwa s_3_sequence.txt > s_3_sequence.txt.sam
		+
		+	* SAMtools http://samtools.sourceforge.net/samtools.shtml
		+
		+	samtools faidx wg.fa
		+	samtools import wg.fa.fai s_3_sequence.txt.sam s_3_sequence.txt.bam
		+	samtools sort s_3_sequence.txt.bam s_3_sequence.txt.srt
		+	samtools index s_3_sequence.txt.srt.bam
		+	samtools pileup -f wg.fa s_3_sequence.txt.srt.bam

Elementolab/SNPseeqer Tutorial

Ole2001 — Sat, 21 Nov 2009 18:49:06 GMT

Revision as of 18:49, 21 November 2009		Current revision
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-	SNPseeqer is a comprehensive software framework for Single Nucleotide Variation (SNV) discovery and characterization from RNA-seq and DNA-seq data. SNPseeqer uses mapped short reads as input (e.g. Eland-mapped reads). It is coded in C (and a bit of Perl) and can process hundred millions of reads on a normal laptop.	+	SNPseeqer is a comprehensive software framework for Single Nucleotide Variation (SNV) discovery and characterization from RNA-seq and DNA-seq data. SNPseeqer uses mapped short reads as input (e.g. Eland-mapped reads). It is coded in C (and a bit of Perl) and can process hundreds of millions of reads on a normal laptop.


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	In the command above, -readdir points to the current directory (.), which contains the read files (reads.chr1, etc). SNPseeqer assumes that all these files are present.		In the command above, -readdir points to the current directory (.), which contains the read files (reads.chr1, etc). SNPseeqer assumes that all these files are present.

-	Additional options:	+	Additional options are as follows. To specify how isolated a mismatch needs to be to be taken into account, use:
-	-rw INT (e.g. 10)	+
-	-uniquereads INT (0 or 1)	+	-rw INT # e.g. 10 would require that mismatch be surrounded by 10 non-mismatches on either side
		+
		+	To merge multiple reads starting at the same genomic position, use:
		+
		+	-uniquereads 1
		+

	* Determine which ones of the SNVs are in known SNPs in dbSNP. This procedure requires that dbSNP be downloaded and split into chromosome files.		* Determine which ones of the SNVs are in known SNPs in dbSNP. This procedure requires that dbSNP be downloaded and split into chromosome files.

-	./dbSNPmatches -mutfile BH_snps.txt > BH_snps_withdbSNP.txt	+	./dbSNPmatches -snvfile BH_snps.txt > BH_snps_withdbSNP.txt

	* Optional: filter out SNVs that do not look like SNPs in dbSNP.		* Optional: filter out SNVs that do not look like SNPs in dbSNP.

-	./filterSNVsUsingdbSNPdata BH_snps_withdbSNP.txt > BH_snps_withdbSNP_filtered.txt	+	./filterSNVsUsingdbSNPdata BH_snps_withdbSNP.txt 1 1 > BH_snps_withdbSNP_filtered.txt

	* Annotate SNVs using RefSeq genes (downloaded from UCSC Genome Browser)		* Annotate SNVs using RefSeq genes (downloaded from UCSC Genome Browser)
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	chr4 108862401 HZ rs16780 NM_005443 - PAPSS1 -1 PROMOTER -1534 bp UPSTREAM OF TSS		chr4 108862401 HZ rs16780 NM_005443 - PAPSS1 -1 PROMOTER -1534 bp UPSTREAM OF TSS
	chr3 9686140 HZ - NM_022485 5 MTMR14 1 CODING CODON=GAT(D) CODONPOS=3 D->E(3X) CODONCHANGE		chr3 9686140 HZ - NM_022485 5 MTMR14 1 CODING CODON=GAT(D) CODONPOS=3 D->E(3X) CODONCHANGE
		+
		+	Additional options (corresponding to different gene annotations) include:
		+
		+	-wgrna FILE
		+	-knowngenes FILE
		+	-aceview FILE

	* Count number of non-dbSNP SNVs per gene:		* Count number of non-dbSNP SNVs per gene:

Elementolab/Deep Sequencing Resources

Ole2001 — Sat, 21 Nov 2009 01:16:13 GMT

Revision as of 01:16, 21 November 2009		Current revision
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	* ChIPseeqer is the lab's comprehensive ChIP-seq analysis framework: http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml		* ChIPseeqer is the lab's comprehensive ChIP-seq analysis framework: http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml

-	* Read alignment tools	+	* BWA http://bio-bwa.sourceforge.net/bwa.shtml
-	http://bio-bwa.sourceforge.net/bwa.shtml	+
		+	To create the index using one of the direwulf fat nodes (using Olivier's GR tools):
		+	gr_1n_fat "bwa index -p hg18bwaidx -a bwtsw wg.fa " bwaindex
		+

	* Kurz et al k-mer counting:		* Kurz et al k-mer counting:

Elementolab/SNPseeqer Tutorial

Ole2001 — Fri, 20 Nov 2009 04:31:18 GMT

Revision as of 04:31, 20 November 2009		Current revision
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	In the command above, -readdir points to the current directory (.), which contains the read files (reads.chr1, etc). SNPseeqer assumes that all these files are present.		In the command above, -readdir points to the current directory (.), which contains the read files (reads.chr1, etc). SNPseeqer assumes that all these files are present.

		+	Additional options:
		+	-rw INT (e.g. 10)
		+	-uniquereads INT (0 or 1)

	* Determine which ones of the SNVs are in known SNPs in dbSNP. This procedure requires that dbSNP be downloaded and split into chromosome files.		* Determine which ones of the SNVs are in known SNPs in dbSNP. This procedure requires that dbSNP be downloaded and split into chromosome files.

Elementolab/Datasets

Ole2001 — Thu, 19 Nov 2009 23:13:24 GMT

Revision as of 23:13, 19 November 2009		Current revision
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	Proteomes		Proteomes
	* RefSeq NP ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/protein/		* RefSeq NP ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/protein/
		+
		+
		+	RNA-seq
		+	* Chris Burge's RNAseq dataset http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12946

Elementolab/Mutation-related Resources

Ole2001 — Thu, 19 Nov 2009 22:44:49 GMT

New page

* http://www.uniprot.org/docs/humsavar

Elementolab/

Ole2001 — Thu, 19 Nov 2009 22:44:35 GMT

Revision as of 22:44, 19 November 2009		Current revision
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	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Install Installation Instructions]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Install Installation Instructions]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Tutorial Tutorial]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/SNPseeqer_Tutorial Tutorial]
		+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Mutation-related_Resources Mutation-related Resources]

Elementolab/Datasets

Ole2001 — Thu, 19 Nov 2009 17:59:39 GMT

Revision as of 17:59, 19 November 2009		Current revision
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	** [http://physiology.med.cornell.edu/faculty/elemento/lab/files/datasets/Hummel_NEJM_DLBCL.txt.GCB_ABC_labels GCB/ABC labels]		** [http://physiology.med.cornell.edu/faculty/elemento/lab/files/datasets/Hummel_NEJM_DLBCL.txt.GCB_ABC_labels GCB/ABC labels]

-	On GEO	+
		+	In GEO
	* centroblast vs centrocytes (CXCR4+ vs CXCR4-) http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE15271		* centroblast vs centrocytes (CXCR4+ vs CXCR4-) http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE15271

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	* hg19 (Feb. 2009) http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.zip		* hg19 (Feb. 2009) http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.zip
	* hg18 (Mar. 2006) http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip		* hg18 (Mar. 2006) http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip
		+
		+
		+	Proteomes
		+	* RefSeq NP ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/protein/
		+

	Hi-C		Hi-C

Elementolab/

Ole2001 — Thu, 19 Nov 2009 17:57:17 GMT

Revision as of 17:57, 19 November 2009		Current revision
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	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Datasets Datasets]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Datasets Datasets]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Mac_Tips Mac tips]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Mac_Tips Mac tips]
-	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Deep-Sequencing Deep-Sequencing]	+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Deep_Sequencing_Resources Deep Sequencing Resources]
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/GeneIdentifiers Gene Identifiers]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/GeneIdentifiers Gene Identifiers]

Special:Log/move

Ole2001 — Thu, 19 Nov 2009 17:56:17 GMT

[[Elementolab/Deep-Sequencing]] moved to [[Elementolab/Deep Sequencing Resources]]

Elementolab/ChIPsmoothedReads2Track

Ole2001 — Wed, 18 Nov 2009 20:31:14 GMT

New page

== ChIPsmoothedReads2Track ==

This analysis helps you smooth read counts across the whole genome (or across a given interval or sets of intervals), and create a read density track.
Using the track in the UCSC Genome Browser allows to visualize what ChIPseeqer peaks look like in the raw data.

1.Go to the ChIPseeqer-1.0 directory

$ cd ChIPseeqer-1.0/

2. Type the command:

./ChIPsmoothedReads2Track --chipdir='''CHIP/''' --trackname='''"Smoothed reads"''' --outfile='''TF_smoothed_reads'''

This command will create a gzipped file name TF_smoothed_reads.gz.

You can then point your Web browser to [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser], and upload the track in the "Add custom tracks" section (or "Manage custom tracks").

Elementolab/ChIPseeqer Tutorial

Ole2001 — Wed, 18 Nov 2009 20:26:58 GMT

Revision as of 20:26, 18 November 2009		Current revision
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	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Track Use ChIPseeqer2Track]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Track Use ChIPseeqer2Track]

-	* Analysis 3: Search for regulatory elements using FIRE	+	* Analysis 3: Smooth read counts across the whole genome (or across a given interval or sets of intervals) and creates a read density track for the UCSC Genome Browser
		+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPsmoothedReads2Track Use ChIPsmoothedReads2Track]
		+
		+	* Analysis 4: Search for regulatory elements using FIRE
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2FIRE Use ChIPseeqer2FIRE]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2FIRE Use ChIPseeqer2FIRE]

-	* Analysis 4: Determine pathways associated with genes using iPAGE	+	* Analysis 5: Determine pathways associated with genes using iPAGE
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2iPAGE Use ChIPseeqer2iPAGE]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2iPAGE Use ChIPseeqer2iPAGE]

-	* Analysis 5: Evaluate conservation of detected peaks	+	* Analysis 6: Evaluate conservation of detected peaks
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Cons Use ChIPseeqer2Cons]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Cons Use ChIPseeqer2Cons]

-	* Analysis 6: Comparing detected peaks between datasets	+	* Analysis 7: Comparing detected peaks between datasets
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Intervals Use Compare Intervals]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Intervals Use Compare Intervals]

-	* Analysis 7: Comparing RefSeq genes between datasets	+	* Analysis 8: Comparing RefSeq genes between datasets
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use Compare Genes]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use Compare Genes]

-	* Analysis 8: Annotate and filter the detected peaks (Repeating elements-RepMasker, CpG islands, Segmental Duplications)	+	* Analysis 9: Annotate and filter the detected peaks (Repeating elements-RepMasker, CpG islands, Segmental Duplications)
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Annotate Use ChIPseeqerAnnotate]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Annotate Use ChIPseeqerAnnotate]