Recent page changes from site "Flux Capacitor" (a Wikidot site)

"Abundance Measures" - source change

Thu, 16 Jun 2011 16:28:55 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 12
Date changed: Thu, 16 Jun 2011 16:28:55 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"Abundance Measures" - source change

Thu, 16 Jun 2011 16:27:26 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 11
Date changed: Thu, 16 Jun 2011 16:27:26 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"Abundance Measures" - source change

Thu, 16 Jun 2011 16:27:09 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 10
Date changed: Thu, 16 Jun 2011 16:27:09 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"BED format" - source change

Thu, 16 Jun 2011 16:22:21 +0000

Page: BED format (formats:bed)
Current revision number: 4
Date changed: Thu, 16 Jun 2011 16:22:21 +0000
Change type: source change
By: gmicha

Page content preview:
The BED (Browser Extensible Data) format has been developed by UCSC for displaying transcript structures in the genome browser, a full description of the format can be found there. The following...

"Fragmentation and filtering" - source change

Thu, 16 Jun 2011 16:20:09 +0000

Page: Fragmentation and filtering (simulator:fragment)
Current revision number: 5
Date changed: Thu, 16 Jun 2011 16:20:09 +0000
Change type: source change
By: gmicha

Page content preview:
Next, an optional fragmentation process (nebulization, hydrolysis, adaptive focusing acoustics, …) may be comprised in the simulation. In general the simulation distinguishes 2 different...

"Fragmentation and filtering" - source change

Thu, 16 Jun 2011 16:19:40 +0000

Page: Fragmentation and filtering (simulator:fragment)
Current revision number: 4
Date changed: Thu, 16 Jun 2011 16:19:40 +0000
Change type: source change
By: gmicha

Page content preview:
Next, an optional fragmentation process (nebulization, hydrolysis, adaptive focusing acoustics, …) may be comprised in the simulation. In general the simulation distinguishes 2 different...

"Sequencing" - source change

Thu, 16 Jun 2011 16:18:15 +0000

Page: Sequencing (simulator:sequence)
Current revision number: 2
Date changed: Thu, 16 Jun 2011 16:18:15 +0000
Change type: source change
By: gmicha

Page content preview:
Requires: LIB_FILE_NAME, READ_LENGTH, READ_NUMBER, PAIRED_END, FASTQ, GEN_DIR, ERR_FILE_NAME, QTHOLD Outputs: SEQ_FILE_NAME This step produces about READ_NUMBER sequencing reads from the library in...

"Parameter file (PAR) format" - source change

Tue, 20 Jul 2010 07:48:29 +0000

Page: Parameter file (PAR) format (formats:par)
Current revision number: 3
Date changed: Tue, 20 Jul 2010 07:48:29 +0000
Change type: source change
By: gmicha

Page content preview:
The format of the PAR (Simulation Parameters) files used by the FLUX SIMULATOR to administrate all parameters of a run. It is a tab-separated 2-column list of key value pairs and comprises the...

"Forum Thread" - file action

Fri, 14 May 2010 19:50:52 +0000

Page: Forum Thread (forum:thread)
Current revision number: 8
Date changed: Fri, 14 May 2010 19:50:52 +0000
Change type: file action
Change comments: Uploaded multiple files.
By: gmicha

Page content preview:

"Error model (ERR) format" - source change

Fri, 14 May 2010 18:09:39 +0000

Page: Error model (ERR) format (formats:err)
Current revision number: 8
Date changed: Fri, 14 May 2010 18:09:39 +0000
Change type: source change
By: gmicha

Page content preview:
Important, read this: As by build 20090729 of the Simulator, the .ERR format has changed to allow for both, quality-based models and such without. The article here describes the new version...

"Error model (ERR) format" - source change

Fri, 14 May 2010 18:09:02 +0000

Page: Error model (ERR) format (formats:err)
Current revision number: 7
Date changed: Fri, 14 May 2010 18:09:02 +0000
Change type: source change
By: gmicha

Page content preview:
Important, read this: As by build 20090729 of the Simulator, the .ERR format has changed to allow for both, quality-based models and such without. The article here describes the new version...

"Parameter file (PAR) format" - source change

Mon, 10 May 2010 13:45:42 +0000

Page: Parameter file (PAR) format (formats:par)
Current revision number: 2
Date changed: Mon, 10 May 2010 13:45:42 +0000
Change type: source change
By: Jennifer Parker

Page content preview:
The format of the PAR (Simulation Parameters) files used by the FLUX SIMULATOR to administrate all parameters of a run. It is a tab-separated 2-column list of key value pairs and comprises the...

"Regular Expressions to describe attributes in read descriptors" - new page

Tue, 27 Apr 2010 19:18:02 +0000

Page: Regular Expressions to describe attributes in read descriptors (formats:regexp)
Current revision number: 0
Date changed: Tue, 27 Apr 2010 19:18:02 +0000
Change type: new page
By: gmicha

Page content preview:
Regular expressions allow for a flexible description of attribute retrieval from generic read descriptors. A summary of the regular expression system adopted in the Flux Capacitor can be found...

"Barcelona Attributes for RNA-Seq (BARNA)" - source change, title change

Tue, 27 Apr 2010 18:42:33 +0000

Page: Barcelona Attributes for RNA-Seq (BARNA) (formats:barna)
Current revision number: 2
Date changed: Tue, 27 Apr 2010 18:42:33 +0000
Change type: source change, title change
By: gmicha

Page content preview:
The BARNA (Barcelona Attributes for RNA-Seq) descriptor is a proposition for annotating unique read IDs with additional information yielded from special experiments, e.g., read mates derived from...

"Barcelona Attributes for RNA-Seq (BARNA)" - source change

Tue, 27 Apr 2010 18:35:09 +0000

Page: Barcelona Attributes for RNA-Seq (BARNA) (formats:barna)
Current revision number: 1
Date changed: Tue, 27 Apr 2010 18:35:09 +0000
Change type: source change
By: gmicha

Page content preview:
The BARNA (Barcelona Attributes for RNA-Seq) descriptor is a proposition for annotating unique read IDs with additional information yielded from special experiments, e.g., read mates derived from...

"Barcelona Attributes for RNA-Seq (BARNA)" - new page

Tue, 27 Apr 2010 18:18:51 +0000

Page: Barcelona Attributes for RNA-Seq (BARNA) (formats:barna)
Current revision number: 0
Date changed: Tue, 27 Apr 2010 18:18:51 +0000
Change type: new page
By: gmicha

Page content preview:
The BARNA (Barcelona Attributes for RNA-Seq) descriptor is a proposition for annotating unique read IDs with additional information yielded from special experiments, e.g., read mates derived from...

"Formats" - source change

Tue, 27 Apr 2010 18:08:07 +0000

Page: Formats (formats)
Current revision number: 46
Date changed: Tue, 27 Apr 2010 18:08:07 +0000
Change type: source change
By: gmicha

Page content preview:
Read Descriptors The BARNA Descriptor The BARNA (Barcelona Attributes for RNA-Seq) descriptor is a proposition for annotating unique read IDs with additional information yielded from special...

"Formats" - source change

Tue, 27 Apr 2010 18:06:52 +0000

Page: Formats (formats)
Current revision number: 45
Date changed: Tue, 27 Apr 2010 18:06:52 +0000
Change type: source change
By: gmicha

Page content preview:
Read Descriptors The BARNA Descriptor The BARNA (Barcelona Attributes for RNA-Seq) descriptor is a proposition for annotating unique read IDs with additional information yielded from special...

"Error model (ERR) format" - source change

Thu, 22 Apr 2010 19:52:09 +0000

Page: Error model (ERR) format (formats:err)
Current revision number: 6
Date changed: Thu, 22 Apr 2010 19:52:09 +0000
Change type: source change
By: gmicha

Page content preview:
Important, read this: As by build 20090729 of the Simulator, the .ERR format has changed to allow for both, quality-based models and such without. The article here describes the new version...

"scratch" - new page

Fri, 05 Mar 2010 02:28:21 +0000

Page: scratch (scratch)
Current revision number: 0
Date changed: Fri, 05 Mar 2010 02:28:21 +0000
Change type: new page
By: gmicha

Page content preview:
(1) \begin{align} p=exp^{-\frac{len_2}{\lambda}} \end{align}

"test" - new page

Sat, 30 Jan 2010 20:29:49 +0000

Page: test (test)
Current revision number: 0
Date changed: Sat, 30 Jan 2010 20:29:49 +0000
Change type: new page
By: gmicha

Page content preview:
test $G=(V,E)$ test

"Flux Mapped Read Descriptor (FMRD)" - source change

Mon, 24 Aug 2009 22:26:00 +0000

Page: Flux Mapped Read Descriptor (FMRD) (formats:fmrd)
Current revision number: 7
Date changed: Mon, 24 Aug 2009 22:26:00 +0000
Change type: source change
By: gmicha

Page content preview:
The Flux Mapped Read Descriptor is adopted by different file formats to condense all relevant information of a mapped read in form of a string, usually stored as read identifier or descriptor. It...

"Flux Mapped Read Descriptor (FMRD)" - source change

Mon, 24 Aug 2009 22:23:12 +0000

Page: Flux Mapped Read Descriptor (FMRD) (formats:fmrd)
Current revision number: 6
Date changed: Mon, 24 Aug 2009 22:23:12 +0000
Change type: source change
By: gmicha

Page content preview:
The Flux Mapped Read Descriptor is adopted by different file formats to condense all relevant information of a mapped read in form of a string, usually stored as read identifier or descriptor. It...

"Flux Mapped Read Descriptor (FMRD)" - source change

Mon, 24 Aug 2009 22:17:08 +0000

Page: Flux Mapped Read Descriptor (FMRD) (formats:fmrd)
Current revision number: 5
Date changed: Mon, 24 Aug 2009 22:17:08 +0000
Change type: source change
By: gmicha

Page content preview:
The Flux Mapped Read Descriptor is adopted by different file formats to condense all relevant information of a mapped read in form of a string, usually stored as read identifier or descriptor. It...

"Sequencing" - source change

Mon, 24 Aug 2009 22:15:31 +0000

Page: Sequencing (simulator:sequence)
Current revision number: 1
Date changed: Mon, 24 Aug 2009 22:15:31 +0000
Change type: source change
By: gmicha

Page content preview:
Requires: LIB_FILE_NAME, READ_LENGTH, READ_NUMBER, PAIRED_END, FASTQ, GEN_DIR, ERR_FILE_NAME, QTHOLD Outputs: SEQ_FILE_NAME This step produces about READ_NUMBER sequencing reads from the library in...

"Abundance Measures" - source change

Thu, 20 Aug 2009 01:15:49 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 9
Date changed: Thu, 20 Aug 2009 01:15:49 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"Abundance Measures" - file action

Thu, 20 Aug 2009 01:14:03 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 8
Date changed: Thu, 20 Aug 2009 01:14:03 +0000
Change type: file action
Change comments: Uploaded file "all_split_unique".
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"Abundance Measures" - source change

Thu, 20 Aug 2009 01:10:22 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 7
Date changed: Thu, 20 Aug 2009 01:10:22 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...

"Flux Capacitor Manual" - source change

Thu, 13 Aug 2009 21:27:28 +0000

Page: Flux Capacitor Manual (capacitor)
Current revision number: 9
Date changed: Thu, 13 Aug 2009 21:27:28 +0000
Change type: source change
By: gmicha

Page content preview:
Version New Features Bugs To Do The list is not sorted by priority output reads observed in Introns command-line flag to deactivate prediction / deconvolution enable gene_id for sub-locus...

"Abundance Measures" - source change

Thu, 13 Aug 2009 21:26:02 +0000

Page: Abundance Measures (capacitor:abundances)
Current revision number: 6
Date changed: Thu, 13 Aug 2009 21:26:02 +0000
Change type: source change
By: gmicha

Page content preview:
Measurements Different measures can be thought of for measuring abundances of RNA features, in general loci, genes, transcripts, exons, or alternative splicing events. In the following the terms...