QCOutputFormat - Revision history

Sgupta at 18:44, 6 July 2010

2010-07-06T18:44:15Z

Sgupta at 01:23, 20 June 2009

2009-06-20T01:23:29Z

Sgupta: /* QCReport Format */

2009-06-20T01:00:12Z

‎QCReport Format

Sgupta at 00:57, 20 June 2009

2009-06-20T00:57:04Z

Sgupta at 19:32, 19 May 2009

2009-05-19T19:32:18Z

Sgupta at 19:31, 19 May 2009

2009-05-19T19:31:56Z

Sgupta at 19:29, 19 May 2009

2009-05-19T19:29:17Z

Sgupta at 19:23, 19 May 2009

2009-05-19T19:23:36Z

Sgupta at 19:10, 19 May 2009

2009-05-19T19:10:44Z

New page

== QCReport Format ==

{| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid white; height:100px" align="center"
|-
| [[image:QualityReport.jpg|center]]
|-
|}

@@ Line 16: / Line 16: @@
 Column 1: Lane #/Sample id <br>
 Column 2: Total # of unique reads (i.e. if a read is repeated in the dataset, it is not counted)<br>
-Column 3: Total # of unique reads AFTER FILTERING (Please refer to FAQ for questions on filtering)<br>
+Column 3: Total # of unique reads AFTER FILTERING (Please refer to [http://jura.wi.mit.edu/genomecorewiki/index.php/Sumeet_Gupta#Do_we_filter_.22bad.22_reads_from_the_final_dataset.3F_.5B06.2F19.2F09.5D| FAQ] for questions on filtering)<br>
 Column 4: Total # of reads in the dataset<br>
-Column 5: Total # of reads IN FILTERED READS (Please refer to FAQ for questions on filtering)<br>
+Column 5: Total # of reads IN FILTERED READS (Please refer to [http://jura.wi.mit.edu/genomecorewiki/index.php/Sumeet_Gupta#Do_we_filter_.22bad.22_reads_from_the_final_dataset.3F_.5B06.2F19.2F09.5D| FAQ] for questions on filtering)<br>
 == Brown Box (QCReport using Base Quality) ==

@@ Line 1: / Line 1: @@
 = QCReport Format =
@@ Line 10: / Line 13: @@
-== Yellow Box ==
+== Yellow Box (QCReport using Base Quality) ==
 Column 1: Lane #/Sample id <br>
 Column 2: Total # of unique reads (i.e. if a read is repeated in the dataset, it is not counted)<br>
-Column 3: Total # of unique reads AFTER FILTERING (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 3: Total # of unique reads AFTER FILTERING (Please refer to FAQ for questions on filtering)<br>
 Column 4: Total # of reads in the dataset<br>
-Column 5: Total # of reads IN FILTERED READS (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 5: Total # of reads IN FILTERED READS (Please refer to FAQ for questions on filtering)<br>
-== Green Box ==
+== Brown Box (QCReport using Base Quality) ==
 Column 1: Lane #/Sample id<br>
 Column 2: Type of Dataset (filtered or not) (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
 Column 3: Total # of reads in the dataset with Tag/Linker <br>
 Column 4: PERCENT Total # of reads in the dataset with Tag/Linker <br>
-Column 5: Unique # of reads in the dataset with Tag/Linker (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 5: Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)<br>
-Column 5: PERCENT Unique # of reads in the dataset with Tag/Linker (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 5: PERCENT Unique # of reads in the dataset with Tag/Linker (Please refer to the FAQ for questions on filtering)<br>
-== Orange Box ==
+== Green Box (QCReport using Base Quality) ==
 Column 1: Lane #/Sample id<br>
 Column 2: Total # of Adaptor Reads<br>
@@ Line 32: / Line 40: @@
 Column 5: PERCENT Total # of PolyA Reads<br>
-== Purple Box ==
+== Grey Box (QCReport using Base Quality) ==
 Column 1: Lane #/Sample id<br>
-Column 2: Type of Dataset (filtered or not) (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)<br>
 Column 3: Percentage of bases with a quality score of atleast 20 (i.e. the probability of base call being incorrect is 1 in a 100)<br>
-== Purple Box ==
+== Purple Box (QCReport using Base Quality) ==
 Column 1: Lane #/Sample id<br>
-Column 2: Type of Dataset (filtered or not) (Please refer to the Solexa Sample Processing Details OR FAQ for questions on filtering)<br>
+Column 2: Type of Dataset (filtered or not) (Please refer to the FAQ for questions on filtering)<br>
 Column 3 and further: Percentage of bases with a quality score of atleast 20 in that cycle/position.<br>

@@ Line 3: / Line 3: @@
 {| class="wikitable" style="font-style:italic; font-size:120%; width:100%; border:2px solid white; height:100px" align="center"
 |-
-| [[image:QualityReport.jpg|center|thumb|500px]]
+| [[image:QualityReport.jpg|QCReport using Base Quality|center|thumb|500px]]
+|
-| [[image:QualityReport.jpg|center|thumb|500px]]
+| [[image:ELAND_QC.JPG|ELAND based QC|center|thumb|500px]]
 |-
 |}