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Fri, 16 Sep 2011 07:28:48 -0000

WikiPage Home modified by

Fri, 16 Sep 2011 07:25:00 -0000

--- v8 
+++ v9 
@@ -3,7 +3,7 @@
 
 **Use**:
 
-> python tile_visual_quality.py fastq_file_name image_output_name [--ngrid int --tile int --base int --encoding str]
+> 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

WikiPage Home modified by

Fri, 16 Sep 2011 07:21:27 -0000

--- v7 
+++ v8 
@@ -9,7 +9,7 @@
 
 2. default ngrid is 500, default tile is all
 
-3. if no base position is specified, the median of the score across all [36] bases is used for every read
+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'

WikiPage Home modified by

Fri, 16 Sep 2011 07:20:45 -0000

--- v6 
+++ v7 
@@ -13,11 +13,11 @@
 
 4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
 
-5. Example:
-
+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'
-
-6. Requires python packages argparse, sys, matplotlib, numpy
 
 
 **Links**:

WikiPage Home modified by

Fri, 16 Sep 2011 07:20:03 -0000

WikiPage Home modified by

Fri, 16 Sep 2011 07:19:40 -0000

--- v4 
+++ v5 
@@ -1,25 +1,26 @@
 - 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:
+**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 [36] bases is used for every read
 
 4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
 
 5. Example:
 
 > python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
 
 6. Requires python packages argparse, sys, matplotlib, numpy
 
 
-Links:
+**Links**:
 
 [FASTQ format](http://en.wikipedia.org/wiki/FASTQ_format)
 [Score encoding](http://en.wikipedia.org/wiki/FASTQ_format#Variations)

WikiPage Home modified by

Fri, 16 Sep 2011 07:16:49 -0000

--- v3 
+++ v4 
@@ -2,18 +2,19 @@
 - 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]
-
+> 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 [36] bases is used for every read
 
 4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
 
 5. Example:
->> python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
+
+> python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
 
 6. Requires python packages argparse, sys, matplotlib, numpy

WikiPage Home modified by

Fri, 16 Sep 2011 07:16:11 -0000

--- v2 
+++ v3 
@@ -3,6 +3,7 @@
 
 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

WikiPage Home modified by

Fri, 16 Sep 2011 07:15:08 -0000

--- v1 
+++ v2 
@@ -1,5 +1,23 @@
-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/wiki/markdown_syntax/) syntax.
+- 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 [36] bases is used for every read
+
+4. encoding type: 'sanger', 'illumina1.0' or 'illumina1.3', default is 'illumina1.3'
+
+5. Example:
+>> python tile_visual_quality.py data.fastq tile.png --ngrid 500 --tile 10 --base 5 --encoding 'illumina1.3'
+
+6. Requires python packages argparse, sys, matplotlib, numpy
+
+
+Links:
+
+[FASTQ format](http://en.wikipedia.org/wiki/FASTQ_format)
+[Score encoding](http://en.wikipedia.org/wiki/FASTQ_format#Variations)

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/wiki/markdown_syntax/) syntax.