Sumeet Gupta - Revision history

Sgupta: Replaced content with "{| style="text-align: left; width:90%" | right Sumeet Gupta
Bioinformatics and Sequencing Supervisor,
Phone: 617-324-0339..."

2024-01-31T12:53:37Z

Replaced content with "{| style="text-align: left; width:90%" | right Sumeet Gupta <br> Bioinformatics and Sequencing Supervisor, <br> Phone: 617-324-0339..."

Show changes

Sgupta at 12:53, 31 January 2024

2024-01-31T12:53:16Z

Sgupta at 16:48, 27 October 2010

2010-10-27T16:48:37Z

Sgupta at 21:55, 8 April 2010

2010-04-08T21:55:56Z

Sgupta at 21:55, 8 April 2010

2010-04-08T21:55:40Z

Sgupta at 21:55, 8 April 2010

2010-04-08T21:55:25Z

Sgupta at 21:54, 8 April 2010

2010-04-08T21:54:20Z

Sgupta at 21:52, 8 April 2010

2010-04-08T21:52:01Z

Sgupta at 21:51, 8 April 2010

2010-04-08T21:51:35Z

Sgupta at 21:46, 8 April 2010

2010-04-08T21:46:18Z

@@ Line 3: / Line 3: @@
 [[image:Sumeet.jpg|right]]
 [[Sumeet_Gupta| Sumeet Gupta]] <br>
-Bioinformatics Analyst, <br>
+Bioinformatics and Sequencing Supervisor, <br>
 Phone: 617-324-0339 <br>
 Email: sgupta at wi dot mit dot edu <br>

@@ Line 4: / Line 4: @@
 [[Sumeet_Gupta| Sumeet Gupta]] <br>
 Bioinformatics Analyst, <br>
-Phone: 617-258-8803 <br>
+Phone: 617-324-0339 <br>
 Email: sgupta at wi dot mit dot edu <br>
 |}

@@ Line 14: / Line 14: @@
 Yes. The control does allow us to distinguish between a cluster generation/sequencing issue vs a library/sample prep issue. In addition, it is useful to calculate the phasing and prephasing parameters (used to access the sequencing "efficiency") for the solexa base calling step which assumes a random distribution of bases. If we do not have a random distribution, it would lead to wrong base calls and worse quality scores, eventually leading to loss of data.
-=== Do we filter "bad" reads from the final dataset? ===
+=== Do we filter "bad" reads from the final dataset? [06/19/09] ===
 The default Illumina pipeline quality filter is used, which uses a threshold of CHASTITY >= 0.6. Chastity for a given base call is defined as "the ratio of the highest of the four (base type) intensities to the sum of highest two." This filter is used to identify clusters with a low signal to noise ratio, often as a result of two adjacent clusters being so physically close together that their signals cannot be measured independently.
@@ Line 20: / Line 20: @@
 We do NOT remove the filtered reads from the final dataset but we do mark each read ID with a boolean system indicating 1 for good/Not Filered reads and 0 for bad/filtered reads.
-=== Was solexa pipeline version 1.3+ used for processing my data? [06/19/09] ===
+=== Was solexa pipeline version 1.3+ used for processing my data? ===
 Use the "grep" command in unix to do a search for the characters unique to the Solexa older pipeline i.e. any of these characters in red below. If they are, then the data was generated using an older pipeline than 1.3.

@@ Line 14: / Line 14: @@
 Yes. The control does allow us to distinguish between a cluster generation/sequencing issue vs a library/sample prep issue. In addition, it is useful to calculate the phasing and prephasing parameters (used to access the sequencing "efficiency") for the solexa base calling step which assumes a random distribution of bases. If we do not have a random distribution, it would lead to wrong base calls and worse quality scores, eventually leading to loss of data.
-=== Do we filter "bad" reads from the final dataset? [06/19/09] ===
+=== Do we filter "bad" reads from the final dataset? ===
 The default Illumina pipeline quality filter is used, which uses a threshold of CHASTITY >= 0.6. Chastity for a given base call is defined as "the ratio of the highest of the four (base type) intensities to the sum of highest two." This filter is used to identify clusters with a low signal to noise ratio, often as a result of two adjacent clusters being so physically close together that their signals cannot be measured independently.

@@ Line 22: / Line 22: @@
 === Was solexa pipeline version 1.3+ used for processing my data? [06/19/09] ===
-Use the "grep" command in unix to do a search for the characters unique to the Solexa older pipeline i.e. any of these characters - ;<=>?
+Use the "grep" command in unix to do a search for the characters unique to the Solexa older pipeline i.e. any of these characters in red below. If they are, then the data was generated using an older pipeline than 1.3.
     ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................

@@ Line 26: / Line 26: @@
     ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
     ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-    !"#$%&'()*+,-./0123456789:
+    !"#$%&'()*+,-./0123456789:<font color="red">;<=>?</font>@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
     |                         |    |        |                              |                     |
                         59   64       73                            104                   126

← Older revision		Revision as of 21:51, 8 April 2010
Line 19:		Line 19:

	We do NOT remove the filtered reads from the final dataset but we do mark each read ID with a boolean system indicating 1 for good/Not Filered reads and 0 for bad/filtered reads.		We do NOT remove the filtered reads from the final dataset but we do mark each read ID with a boolean system indicating 1 for good/Not Filered reads and 0 for bad/filtered reads.
		+
		+	=== Was solexa pipeline version 1.3+ used for processing my data? [06/19/09] ===
		+
		+	Use the "grep" command in unix to do a search for the characters unique to the Solexa older pipeline i.e. any of these characters - ;<=>?
		+
		+	...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
		+	..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
		+	!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{\|}~
		+	\| \| \| \| \| \|
		+	33 59 64 73 104 126
		+
		+	I - Illumina 1.3 Phred+64, 41 values (0, 40)
		+	X - Solexa Solexa+64, 68 values (-5, 62)
		+	Courtesy: http://en.wikipedia.org/wiki/FASTQ_format
		+

	== Solexa Quality Scores ==		== Solexa Quality Scores ==

@@ Line 45: / Line 45: @@
    Illumina 1.3 Phred+64,  41 values  (0, 40)
    Solexa       Solexa+64, 68 values (-5, 62)
    Courtesy: http://en.wikipedia.org/wiki/FASTQ_format

Sumeet Gupta - Revision history

Sgupta: Replaced content with "{| style="text-align: left; width:90%" | right Sumeet Gupta Bioinformatics and Sequencing Supervisor, Phone: 617-324-0339..."

Sgupta at 12:53, 31 January 2024

Sgupta at 16:48, 27 October 2010

Sgupta at 21:55, 8 April 2010

Sgupta at 21:55, 8 April 2010

Sgupta at 21:55, 8 April 2010

Sgupta at 21:54, 8 April 2010

Sgupta at 21:52, 8 April 2010

Sgupta at 21:51, 8 April 2010

Sgupta at 21:46, 8 April 2010

Sgupta: Replaced content with "{| style="text-align: left; width:90%" | right Sumeet Gupta
Bioinformatics and Sequencing Supervisor,
Phone: 617-324-0339..."