FusionSeq Test Datasets - Revision history

Asboner at 09:38, 7 August 2011

2011-08-07T09:38:40Z

← Older revision		Revision as of 09:38, 7 August 2011
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	{{FusionSeqHeader}}		{{FusionSeqHeader}}
	Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/R104/abstract Genome Biology, 2010;11:R104]. Please note that the full set, including cancer samples, ~~will be~~ available at [http://www.ncbi.nlm.nih.gov/~~sites/entrez~~?db=~~gap~~ dbGaP] ~~soon~~, where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:		Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/R104/abstract Genome Biology, 2010;11:R104]. Please note that the full set, including cancer tissue samples, is available at [http://www.ncbi.nlm.nih.gov/gap?term=phs000311.v1.p1 dbGaP (accession phs000311.v1.p1)], where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:

	==[[RSEQtools#Mapped_Read_Format (MRF)\|Mapped Read Format (MRF)]]==		==[[RSEQtools#Mapped_Read_Format (MRF)\|Mapped Read Format (MRF)]]==

Asboner: /* Auxillliary data */

2010-12-08T07:11:18Z

Auxillliary data

← Older revision		Revision as of 07:11, 8 December 2010
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	Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.		Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.

	[[FusionSeq_List of ~~Programs~~#~~gfrBlackListFilter~~\|gfrBlackListFilter]] allows you to specify a list of candidates to be excluded. The tab-delimited file includes only the gene symbols of the two genes, such as:		[[FusionSeq_List of programs#gfrBlacklistFilter\|gfrBlackListFilter]] allows you to specify a list of candidates to be excluded. The tab-delimited file includes only the gene symbols of the two genes, such as:
	LOC388160 LOC388161		LOC388160 LOC388161
	LOC388161 LOC388161		LOC388161 LOC388161

Asboner: /* Auxillliary data */

2010-12-08T07:07:42Z

Auxillliary data

← Older revision		Revision as of 07:07, 8 December 2010
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	* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660_allReads.txt.gz NCIH660_allReads.txt.gz]		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660_allReads.txt.gz NCIH660_allReads.txt.gz]
	Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.		Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.

			[[FusionSeq_List of Programs#gfrBlackListFilter\|gfrBlackListFilter]] allows you to specify a list of candidates to be excluded. The tab-delimited file includes only the gene symbols of the two genes, such as:
			LOC388160 LOC388161
			LOC388161 LOC388161

			An example of a blacklist file can be downloaded [http://rnaseq.gersteinlab.org/fusionseq/datasets/blackList.txt here].

	==FASTQ==		==FASTQ==

Asboner: /* Auxillliary data */

2010-12-03T12:16:15Z

Auxillliary data

← Older revision		Revision as of 12:16, 3 December 2010
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	* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.meta GM12878.meta]		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.meta GM12878.meta]
	* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.meta NCIH660.meta]		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.meta NCIH660.meta]

			'''NB:''' please make sure that the *meta files are tab delimited.

	The junction sequence identifier module requires to align all reads against the junction library. All the reads, including those that did not map, should be used to find as much support for the breakpoint junction.		The junction sequence identifier module requires to align all reads against the junction library. All the reads, including those that did not map, should be used to find as much support for the breakpoint junction.

Asboner at 08:09, 3 November 2010

2010-11-03T08:09:40Z

@@ Line 6: / Line 6: @@
 * [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.mrf.gz GM12878.mrf.gz]
 * [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.mrf.gz NCIH660.mrf.gz]
 Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.

Asboner: /* BAM */

2010-10-23T22:11:11Z

BAM

← Older revision		Revision as of 22:11, 23 October 2010
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	==BAM==		==BAM==
	[http://samtools.sourceforge.net/ BAM] format is the binary compressed format of [http://samtools.sourceforge.net/ SAM (Sequence Alignment/Map)]. We provide both BAM files and their corresponding index files (*.bai) so that they can be viewed with the [http://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] a high-performance visualization tool for interactive exploration of large, integrated datasets from the Broad Institute.		[http://samtools.sourceforge.net/ BAM] format is the binary compressed format of [http://samtools.sourceforge.net/ SAM (Sequence Alignment/Map)]. We provide both BAM files and their corresponding index files (*.bai) so that they can be viewed with the [http://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] a high-performance visualization tool for interactive exploration of large, integrated datasets from the Broad Institute.
	* http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam]
	* http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam.bai		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam.bai http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam.bai]
	* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam]
	* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai		* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai]
	You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.		You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.

Asboner at 21:03, 23 October 2010

2010-10-23T21:03:37Z

← Older revision		Revision as of 21:03, 23 October 2010
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			{{FusionSeqHeader}}
	Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/R104/abstract Genome Biology, 2010;11:R104]. Please note that the full set, including cancer samples, will be available at [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap dbGaP] soon, where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:		Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/R104/abstract Genome Biology, 2010;11:R104]. Please note that the full set, including cancer samples, will be available at [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap dbGaP] soon, where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:

Asboner at 21:02, 23 October 2010

2010-10-23T21:02:19Z

← Older revision		Revision as of 21:02, 23 October 2010
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	* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai		* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai
	You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.		You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.

	~~==Prostate cancer dataset==~~
	~~The dataset mentioned in the publication [http:~~

Asboner: Created page with 'Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/…'

2010-10-23T20:59:11Z

Created page with 'Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/…'

New page

Two datasets are available to test FusionSeq: NCIH660 and GM12878 cell-line data. These datasets are part of FusionSeq dataset, published in [http://genomebiology.com/2010/11/10/R104/abstract Genome Biology, 2010;11:R104]. Please note that the full set, including cancer samples, will be available at [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap dbGaP] soon, where confidentiality issues are taken care of properly. We here provide the cell-line data in different formats:

==[[RSEQtools#Mapped_Read_Format (MRF)|Mapped Read Format (MRF)]]==
This is the format required by FusionSeq. [http://rseqtools.gersteinlab.org/ RSEQtools] provide several conversion tools to generate MRF files from the most popular alignment tools.
* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.mrf.gz GM12878.mrf.gz]
* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.mrf.gz NCIH660.mrf.gz]
Please read '[[How to execute FusionSeq]]' section for more detail on how to use these files.

==FASTQ==
[http://en.wikipedia.org/wiki/FASTQ_format FASTQ] is a text-based format for storing both a biological sequence and its corresponding quality scores. Each tarball includes two FASTQ files, one for each end.
* [http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.fastq.tar.gz GM12878.fastq.tar.gz]
* [http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.fastq.tar.gz NCIH660.fastq.tar.gz]

==BAM==
[http://samtools.sourceforge.net/ BAM] format is the binary compressed format of [http://samtools.sourceforge.net/ SAM (Sequence Alignment/Map)]. We provide both BAM files and their corresponding index files (*.bai) so that they can be viewed with the [http://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] a high-performance visualization tool for interactive exploration of large, integrated datasets from the Broad Institute.
* http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam
* http://rnaseq.gersteinlab.org/fusionseq/datasets/GM12878.bam.bai
* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam
* http://rnaseq.gersteinlab.org/fusionseq/datasets/NCIH660.bam.bai
You can download the files locally or load them into IGV directly. See instructions at http://www.broadinstitute.org/igv/.

==Prostate cancer dataset==
The dataset mentioned in the publication [http: