DiffKAP - Revision history

Uqccha18: /* Download */

2017-08-14T08:26:35Z

‎Download

Uqccha18 at 02:53, 11 September 2015

2015-09-11T02:53:48Z

Philippbayer: Undo revision 580 by Philippbayer (talk)

2014-04-28T04:15:26Z

Undo revision 580 by Philippbayer (talk)

Philippbayer: Undo revision 581 by Philippbayer (talk)

2014-04-28T04:15:16Z

Undo revision 581 by Philippbayer (talk)

Philippbayer at 06:02, 27 April 2014

2014-04-27T06:02:35Z

Philippbayer at 05:45, 27 April 2014

2014-04-27T05:45:50Z

Uqccha18: /* Download */

2013-09-23T04:19:13Z

‎Download

Uqccha18: /* How to interpret the results? */

2013-09-23T04:18:23Z

‎How to interpret the results?

Uqccha18: /* How to install? */

2013-09-23T04:18:10Z

‎How to install?

Uqccha18 at 04:15, 23 September 2013

2013-09-23T04:15:56Z

@@ Line 22: / Line 22: @@
 == Download ==
 * Latest Version 0.9 (23/09/2013):
-** [http://appliedbioinformatics.com.au/download/DiffKAP_0.9.zip DiffKAP package]
+** [http://appliedbioinformatics.com.au/download/DiffKAP/DiffKAP_0.9.zip DiffKAP package]
-** [http://appliedbioinformatics.com.au/download/sampleProj_results.tar.gz Results of the sample data]
+** [http://appliedbioinformatics.com.au/download/DiffKAP/DiffKAP_sampleProj_testData.tar.gz Test Data]
 * Archived Versions:
 **

@@ Line 69: / Line 69: @@
 == Reference ==
 * Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.
 Back to [[Main_Page]]

@@ Line 3: / Line 3: @@
 With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.
-The DiffKAP application consists of a series of scripts written in Python, Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.
+The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.
@@ Line 18: / Line 18: @@
 ** Config::IniFiles
 ** GD::Graph::linespoints  (for the script identifyKmerSize)
-* optional: SOAPaligner for mapping reads to a (again, optional) reference
 == Download ==
@@ Line 35: / Line 35: @@
 ** an example data folder containing a small subset of a metatranscriptomic data
 * read the README
-* Install the DiffKAP setup script by executing: DiffKAP_setup (does this exist? - Philipp)
+* Install the DiffKAP setup script by executing: DiffKAP_setup
 * *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***
 == How to run? ==
 # Create your project configuration file by using the example config file in the sample data directory as a template.
 # Run the pipeline: Run DiffKAP with your config file as an input argument, for example: DiffKAP ~/sampleProj/sampleProj.cfg
-* Optionally, the pipeline can generate SOAP-alignments if the user supplies a reference in the configuration file
+* Results will be generated in the [OUT_DIR]/results where [OUT_DIR] is defined in the config file.
 * The processing log is stored in /tmp/DiffKAP.log by default.
 == How to interpret the results? ==
 * You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
-* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/PARs:
+* The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
 *# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
 *#* Median-T1: The median k-mer occurrence represented in Treatment 1 (corresponding to T1_ID in the config file) for all kmers in the read.
@@ Line 76: / Line 69: @@
 == Reference ==
 * Marçais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764-770.
-* A paper for the optimal k-mer count?
 Back to [[Main_Page]]

@@ Line 3: / Line 3: @@
 With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.
-The DiffKAP application consists of a series of scripts written in Python, Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and, optionally, SOAPaligner. The scripts are freely available for non-commercial use.
+The DiffKAP application consists of a series of scripts written in Python, Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.
 == What does DiffKAP depend on? ==
@@ Line 10: / Line 11: @@
 * blastx for sequence alignment
 * Some non-standard Perl modules:
-** BioPerl
+** bioperl
 *** Bio::SeqIO
 *** Bio::SearchIO
@@ Line 17: / Line 18: @@
 ** Config::IniFiles
 ** GD::Graph::linespoints  (for the script identifyKmerSize)
-* Some non-standard Python modules:
+* optional: SOAPaligner for mapping reads to a (again, optional) reference
 == Download ==

@@ Line 3: / Line 3: @@
 With the lack of reference assemblies currently limiting meta-transcriptome studies, we have established a Differential k-mer Analysis Pipeline (DiffKAP) for gene expression analysis, which does not require the generation of a reference for read mapping. By reducing each read to component k-mers and comparing the relative abundance of these sub-sequences, we overcome statistical limitations of whole read comparative analysis.
-The DiffKAP application consists of a series of scripts written in Python, Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of a blast-formatted protein database. The scripts are freely available for non-commercial use.
+The DiffKAP application consists of a series of scripts written in Python, Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and, optionally, SOAPaligner. The scripts are freely available for non-commercial use.
 == What does DiffKAP depend on? ==
@@ Line 11: / Line 10: @@
 * blastx for sequence alignment
 * Some non-standard Perl modules:
-** bioperl
+** BioPerl
 *** Bio::SeqIO
 *** Bio::SearchIO
@@ Line 18: / Line 17: @@
 ** Config::IniFiles
 ** GD::Graph::linespoints  (for the script identifyKmerSize)
-* optional: SOAPaligner for mapping reads to a (again, optional) reference
+* Some non-standard Python modules:
 == Download ==

@@ Line 46: / Line 46: @@
 == How to interpret the results? ==
-* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download here].
+* You can download the results of the sample data [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download here].
 * The script "DiffKAP" generates 4 types of files in folder [OUT_DIR]/results:
 *# 5 DER files with the word 'AllDER' in the filenames. Explanation of some columns:
@@ Line 61: / Line 61: @@
 *#* It is sorted by the 'Total' column in reversed order.
 *# A result summary file with 'summary.log' in the filename.
 == FAQ ==

@@ Line 28: / Line 28: @@
 == How to install? ==
-* Download the [http://www.appliedbioinformatics.com.au/index.php?title=DiffKAP&action=submit#Download DiffKAP package].
+* Download the [http://www.appliedbioinformatics.com.au/index.php/DiffKAP#Download DiffKAP package].
 * Uncompress it into:
 ** a DiffKAP setup file
@@ Line 37: / Line 37: @@
 * Install the DiffKAP setup script by executing: DiffKAP_setup
 * *** If you like, you can add the DiffKAP path to $PATH or just use an absolute path for running DiffKAP ***
 == How to run? ==