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Home modified by Wenwei

Wenwei — Mon, 23 Sep 2013 14:15:51 -0000

--- v8
+++ v9
@@ -119,7 +119,7 @@
   grade 1 ratio, i.e. TH_G1 (1.5)
   grade 2 ratio, i.e. TH_G2 (3)

-Please consult the 'application.conf' file for detailed parameters and configuration.
+Please consult the **'application.conf'** file for detailed parameters and configuration.

 ## ======== Result interpretation ========

Home modified by Wenwei

Wenwei — Mon, 23 Sep 2013 14:12:59 -0000

--- v7
+++ v8
@@ -1,4 +1,4 @@
-# InsertionMapper v1.0 -- 09/20/2013
+# InsertionMapper v1.1 -- 09/20/2013

 Copyright (c) 2013 Wenwei Xiong

Home modified by Wenwei

Wenwei — Mon, 23 Sep 2013 14:12:43 -0000

--- v6
+++ v7
@@ -1,4 +1,4 @@
-# InsertionMapper v1.0 -- 05/20/2013
+# InsertionMapper v1.0 -- 09/20/2013

 Copyright (c) 2013 Wenwei Xiong

@@ -23,6 +23,8 @@
 #### \[FOR REVIEWERS]

 Please click [InsertionMapper](http://sourceforge.net/projects/insertionmapper/files/InsertionMapper_%28Test%20data%20included%29.zip/download) to download the latest InsertionMapper, with test data included. 
+
+A bigger test dataset in our real [project](http://acdsinsertions.org/) is available at this [link](ftp://bo.csam.montclair.edu/InsertionMapper/test_data/).

 ** For normal users, a different download link will be provided shortly. **

@@ -88,7 +90,7 @@
 3 respectively. All parameters can be changed by modifying 'application.conf'
 file (with illustrations).

-## ======== Configuration ========
+## ===== Configuration and parameters =====

 InsertionMapper is suitable for various scenarios for sequence identification in
 multidimensional pools because of the flexibility of configuration. All
@@ -97,6 +99,27 @@
 be intuitive for users to modify parameters for InsertionMapper without digging
 into the detailed HOCON specification
 (https://github.com/typesafehub/config/blob/master/HOCON.md).
+
+#### A list of common parameters, with values (in parentheses) used in the Dsg project:
+
+**Dimensions**
+  count of dimensions (3)
+  names of dimensions (Plate, Row, Column)
+  number of libraries for each dimension (\[10, 8,12])
+
+**Primers** 
+  primer name (ds17)
+  primer sequence ( ds17 = """CCGACCGTTTTCATCCCTA((.{8}).+)""" ) - in [java regular expression syntax](http://docs.oracle.com/javase/tutorial/essential/regex/), (.{8}) for 8-bp long TSD (target site duplication) as the index sequence for database manipulation. 
+
+**File mapping**
+  directory of raw read files (./raw)
+  a list of file names of raw reads
+  
+**Thresholds** - definitions in the paper
+  grade 1 ratio, i.e. TH_G1 (1.5)
+  grade 2 ratio, i.e. TH_G2 (3)
+  
+Please consult the 'application.conf' file for detailed parameters and configuration.

 ## ======== Result interpretation ========

Home modified by Wenwei

Wenwei — Tue, 21 May 2013 15:24:43 -0000

--- v5
+++ v6
@@ -18,12 +18,19 @@
 is included in InsertionMapper package. 
 See 'GNU_GENERAL_PUBLIC_LICENSE.txt' for more information.

+## ======== Download ========
+
+#### \[FOR REVIEWERS]
+
+Please click [InsertionMapper](http://sourceforge.net/projects/insertionmapper/files/InsertionMapper_%28Test%20data%20included%29.zip/download) to download the latest InsertionMapper, with test data included. 
+
+** For normal users, a different download link will be provided shortly. **

 ## ======== Installation ========

 InsertionMapper is developed on the Java Virtual Machine (JVM) platform. Users
 can easily download the zip file and unzip it to a local directory. No
-compilation is needed, thanks to JVM's cross platform compatibility.
+compilation is needed thanks to JVM's cross platform compatibility.

 ## ======== System requirements ========

Home modified by Wenwei

Wenwei — Tue, 21 May 2013 02:20:13 -0000

--- v4
+++ v5
@@ -5,9 +5,11 @@
 Welcome to InsertionMapper project!

 Thank you for using InsertionMapper. If you find it useful for your work, please
-cite our paper: Wenwei Xiong, Limei He, Yubin Li, Hugo K. Dooner, Chunguang Du
+cite our paper: 
+
+> ** Wenwei Xiong, Limei He, Yubin Li, Hugo K. Dooner, Chunguang Du
 (2013) InsertionMapper: a pipeline tool for the identification of targeted
-sequences from multidimensional high throughput sequencing data
+sequences from multidimensional high throughput sequencing data **

 The latest version of InsertionMapper is freely accessible at our website:
 https://sourceforge.net/p/insertionmapper

Home modified by Wenwei

Wenwei — Tue, 21 May 2013 02:17:05 -0000

--- v3
+++ v4
@@ -1,4 +1,4 @@
-# InsertionMapper v1.0 -- 05/10/2013
+# InsertionMapper v1.0 -- 05/20/2013

 Copyright (c) 2013 Wenwei Xiong

@@ -10,7 +10,7 @@
 sequences from multidimensional high throughput sequencing data

 The latest version of InsertionMapper is freely accessible at our website:
-http://bo.csam.montclair.edu/du/insertionmapper
+https://sourceforge.net/p/insertionmapper

 The software is open source and distributed under the GNU public license, which
 is included in InsertionMapper package.

Home modified by Wenwei

Wenwei — Mon, 20 May 2013 19:45:43 -0000

--- v2
+++ v3
@@ -1,6 +1,8 @@
-InsertionMapper v1.0 -- 05/10/2013
+# InsertionMapper v1.0 -- 05/10/2013

 Copyright (c) 2013 Wenwei Xiong
+
+Welcome to InsertionMapper project!

 Thank you for using InsertionMapper. If you find it useful for your work, please
 cite our paper: Wenwei Xiong, Limei He, Yubin Li, Hugo K. Dooner, Chunguang Du
@@ -13,17 +15,15 @@
 The software is open source and distributed under the GNU public license, which
 is included in InsertionMapper package. 
 See 'GNU_GENERAL_PUBLIC_LICENSE.txt' for more information.
-# InsertionMapper

-Welcome to InsertionMapper project!

-======== Installation ========
+## ======== Installation ========

 InsertionMapper is developed on the Java Virtual Machine (JVM) platform. Users
 can easily download the zip file and unzip it to a local directory. No
 compilation is needed, thanks to JVM's cross platform compatibility.

-======== System requirements ========
+## ======== System requirements ========

 InsertionMapper requires JRE 1.6+. A full list of Oracle Certified Configuration
 for Java SE 6 can be found at
@@ -37,7 +37,7 @@
 don't need Scala to run the program, unless they want to compile from source
 codes. Please refer to http://www.scala-lang.org/ for details about Scala.

-======== Quick start ========
+## ======== Quick start ========

 The directory structure of InsertionMapper would be like:
 .
@@ -68,7 +68,7 @@
 reads will be generated into 'filtered' directory, and a H2 database named
 'test.db' will be in the top folder.

-======== Introduction ========
+## ======== Introduction ========

 As seen in directory structure, the "InsertionMapper.jar" file encapsulates all
 the essential logics of this pipeline tool, complemented by third-party
@@ -79,7 +79,7 @@
 3 respectively. All parameters can be changed by modifying 'application.conf'
 file (with illustrations).

-======== Configuration ========
+## ======== Configuration ========

 InsertionMapper is suitable for various scenarios for sequence identification in
 multidimensional pools because of the flexibility of configuration. All
@@ -89,7 +89,7 @@
 into the detailed HOCON specification
 (https://github.com/typesafehub/config/blob/master/HOCON.md).

-======== Result interpretation ========
+## ======== Result interpretation ========

 For each primer configured in 'application.conf' file, one report will be
 finally generated, including all identified sequences amplified by that

Home modified by Wenwei

Wenwei — Mon, 20 May 2013 19:43:48 -0000

--- v1
+++ v2
@@ -1,8 +1,119 @@
-Welcome to your wiki!
+InsertionMapper v1.0 -- 05/10/2013

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+Copyright (c) 2013 Wenwei Xiong

-The wiki uses [Markdown](/p/insertionmapper/wiki/markdown_syntax/) syntax.
+Thank you for using InsertionMapper. If you find it useful for your work, please
+cite our paper: Wenwei Xiong, Limei He, Yubin Li, Hugo K. Dooner, Chunguang Du
+(2013) InsertionMapper: a pipeline tool for the identification of targeted
+sequences from multidimensional high throughput sequencing data

-[[members limit=20]]
-[[download_button]]
+The latest version of InsertionMapper is freely accessible at our website:
+http://bo.csam.montclair.edu/du/insertionmapper
+
+The software is open source and distributed under the GNU public license, which
+is included in InsertionMapper package. 
+See 'GNU_GENERAL_PUBLIC_LICENSE.txt' for more information.
+# InsertionMapper
+
+Welcome to InsertionMapper project!
+
+======== Installation ========
+
+InsertionMapper is developed on the Java Virtual Machine (JVM) platform. Users
+can easily download the zip file and unzip it to a local directory. No
+compilation is needed, thanks to JVM's cross platform compatibility.
+
+======== System requirements ========
+
+InsertionMapper requires JRE 1.6+. A full list of Oracle Certified Configuration
+for Java SE 6 can be found at
+http://www.oracle.com/technetwork/java/javase/system-configurations-135212.html.
+
+To determine your java version, just open a system terminal, and type 'java
+-version' (without quotes). If you haven't installed Java yet, please go to the
+official Java website http://java.com/en/download/.
+
+InsertionMapper is written in Scala, and compiled into Java bytecodes. Users
+don't need Scala to run the program, unless they want to compile from source
+codes. Please refer to http://www.scala-lang.org/ for details about Scala.
+
+======== Quick start ========
+
+The directory structure of InsertionMapper would be like:
+.
+|-- GNU_GENERAL_PUBLIC_LICENSE.txt
+|-- InsertionMapper.jar
+|-- README.txt
+|-- application.conf
+|-- lib
+|   |-- h2-1.3.171.jar
+|   |-- mysql-connector-java-5.1.24-bin.jar
+|   |-- scala-library.jar
+|   |-- slf4j-api-1.6.4.jar
+|   |-- slf4j-nop-1.6.4.jar
+|   |-- slick_2.10-1.0.0.jar
+|   `-- typesafe-config.jar
+|-- raw
+|   |-- 20121217_ZZ_l123_KDI_l4_HD_l5_AZ54_91_l6_05_C4_17_F3.fastq   (test file)
+|   |-- 20121217_ZZ_l123_KDI_l4_HD_l5_AZ54_91_l6_05_P13_17_F3.fastq  (test file)
+|   `-- 20121217_ZZ_l123_KDI_l4_HD_l5_AZ54_91_l6_05_RE_17_F3.fastq   (test file)
+|-- filtered
+|
+Open a terminal and change directory (use 'cd' command) to wherever
+InsertionMapper is placed. 
+
+Then simply type 
+   'java -jar InsetionMapper.jar' 
+to run the test data in 'raw' directory. With default configuration, filtered
+reads will be generated into 'filtered' directory, and a H2 database named
+'test.db' will be in the top folder.
+
+======== Introduction ========
+
+As seen in directory structure, the "InsertionMapper.jar" file encapsulates all
+the essential logics of this pipeline tool, complemented by third-party
+libraries in 'lib' folder for database manipulation and parameter configuration.
+
+'raw' and 'filtered' folders are recommend places for raw reads and filtered
+reads, and the default thresholds for Grade-1 and Grade-2 thresholds are 1.5 and
+3 respectively. All parameters can be changed by modifying 'application.conf'
+file (with illustrations).
+
+======== Configuration ========
+
+InsertionMapper is suitable for various scenarios for sequence identification in
+multidimensional pools because of the flexibility of configuration. All
+parameters and embedded SQL sentences are contained in 'application.conf', which
+is written in HOCON (Human-Optimized Config Object Notation) format. It should
+be intuitive for users to modify parameters for InsertionMapper without digging
+into the detailed HOCON specification
+(https://github.com/typesafehub/config/blob/master/HOCON.md).
+
+======== Result interpretation ========
+
+For each primer configured in 'application.conf' file, one report will be
+finally generated, including all identified sequences amplified by that
+particular primer. The report file is a plain csv (comma-separated values) text
+file which can be opened by any text editor or spreadsheet programs (e.g.
+Microsoft Excel). Count of columns may vary depending on how many dimensions in
+sample pools. 
+
+For typical 3-D pools, columns in report file are explained as
+follows:
+
+"DIMENSION": Well coordinates in multidimension pools, library number in each
+dimension separated by '_'.
+"INDEXSEQ": Identified indexing sequences. (E.g. 8-bp TSD for transposable
+elements) 
+"GRADE": Grade of the identified sequence.
+"RANK_P"/"RANK_R"/"RANK_C": Ranks in each dimension.
+"DIMENSION2"/"RANK2_P"/"RANK2_R"/"RANK2_C": Similar to the above columns,
+indicating the significance of sequence assignment, compared to the second
+possible assignment (e.g. no 2nd assignment or very low ranks suggests good
+quality of the first assignment).
+"FULLSEQ": Full sequence identified.
+"COUNTOFSEQSINWELL": Count of sequences assigned in current well.
+"COUNTOFWELLSFORSEQ": Count of wells the current sequence being assigned to.
+
+Sequences identified with no ambiguities are those whose values in last two
+columns are both 1.

Home modified by Wenwei

Wenwei — Mon, 20 May 2013 19:39:46 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Wenwei (admin)