Recent changes to description

WikiPage description modified by

Thu, 01 Dec 2011 22:10:30 -0000

--- v7 
+++ v8 
@@ -1,4 +1,4 @@
-Simple python code that produces color-coded quality plots based on fastq format read quality scores. Scores are averaged over binned read tile coordinates. Useful for spotting spatial quality patterns. 
+Python script that produces color-coded quality plots based on fastq format read quality scores. Scores are averaged over binned read tile coordinates. Useful for spotting spatial quality patterns. 
 
 
 **Use**:

WikiPage description modified by

Fri, 16 Sep 2011 07:38:59 -0000

--- v6 
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 > python tile_visual_quality.py example_fastq_file.txt test --base 2 --ngrid 200
 
-The second line should produce a file named "test_tile14_base2.png" which looks like this:
-
+The second line should produce a file named "test_tile14_base2.png" which looks like the attachment.
 
 
 **Links**:

WikiPage description modified by

Fri, 16 Sep 2011 07:38:17 -0000

--- v5 
+++ v6 
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-- Plot the quality scores of reads in a tile as color-coded pixels in 2D
-- Read tile numbers, coordinates and scores from a regular fastq file format
-
+Simple python code that produces color-coded quality plots based on fastq format read quality scores. Scores are averaged over binned read tile coordinates. Useful for spotting spatial quality patterns. 
+
+
 **Use**:
 
 > python tile_visual_quality.py fastq_file_name image_output_name \[--ngrid int --tile int --base int --encoding str\]
 
 1. options in [] are optional, --ngrid controls the resolution, --tile selects the tile to be plotted, --base selects the base position for which the score is calculated, range from 0 to k-1, where the read length is k
 
 2. default ngrid is 500, default tile is all
 
 3. if no base position is specified, the median of the score across all (ex: 36) bases is used for every read
 
 4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
 
 5. Requires python packages argparse, sys, matplotlib, numpy
 
 **Example**:
 
 > python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
+
+> python tile_visual_quality.py example_fastq_file.txt test --base 2 --ngrid 200
+
+The second line should produce a file named "test_tile14_base2.png" which looks like this:
+
 
 
 **Links**:

WikiPage description modified by

Fri, 16 Sep 2011 07:37:40 -0000

WikiPage description modified by

Fri, 16 Sep 2011 07:31:36 -0000

--- v3 
+++ v4 
@@ -26,5 +26,4 @@
 [Score encoding](http://en.wikipedia.org/wiki/FASTQ_format#Variations)
 
 
-[[project_admins]]
 [[download_button]]

WikiPage description modified by

Fri, 16 Sep 2011 07:29:58 -0000

--- v2 
+++ v3 
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+- Plot the quality scores of reads in a tile as color-coded pixels in 2D
+- Read tile numbers, coordinates and scores from a regular fastq file format
+
+**Use**:
+
+> python tile_visual_quality.py fastq_file_name image_output_name \[--ngrid int --tile int --base int --encoding str\]
+
+1. options in [] are optional, --ngrid controls the resolution, --tile selects the tile to be plotted, --base selects the base position for which the score is calculated, range from 0 to k-1, where the read length is k
+
+2. default ngrid is 500, default tile is all
+
+3. if no base position is specified, the median of the score across all (ex: 36) bases is used for every read
+
+4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
+
+5. Requires python packages argparse, sys, matplotlib, numpy
+
+**Example**:
+
+> python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
+
+
+**Links**:
+
+[FASTQ format](http://en.wikipedia.org/wiki/FASTQ_format)
+[Score encoding](http://en.wikipedia.org/wiki/FASTQ_format#Variations)
 
 
 [[project_admins]]

WikiPage description modified by

Fri, 16 Sep 2011 07:26:24 -0000

--- v1 
+++ v2 
@@ -1,5 +1,4 @@
-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/fastqvizqual/home/markdown_syntax/) syntax.
+
+
+[[project_admins]]
+[[download_button]]

WikiPage Home modified by

Fri, 16 Sep 2011 05:44:33 -0000

Welcome to your wiki! This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/fastqvizqual/home/markdown_syntax/) syntax.