Template:SBB-Protocols SeqResult - Revision history

JCAnderson at 16:37, 4 March 2009

2009-03-04T16:37:42Z

←Older revision		Revision as of 16:37, 4 March 2009
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	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was correct but matched a different part number.		*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was correct but matched a different part number.
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.		*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.
		+

	4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, bad read, or otherwise. Then:		4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, bad read, or otherwise. Then:

JCAnderson at 16:37, 4 March 2009

2009-03-04T16:37:14Z

←Older revision		Revision as of 16:37, 4 March 2009
Line 19:		Line 19:


-	3) It is a different sequence ~~that~~ what I expected, but it matches another one of our parts. Somehow I tube-switched my samples or got someone else's clone.	+	3) It is a different sequence than what I expected, but it matches another one of our parts. Somehow I tube-switched my samples or got someone else's clone.

	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was. Also, upload the sequence from the read into the wiki following the link in the rightmost column.		*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was. Also, upload the sequence from the read into the wiki following the link in the rightmost column.
Line 27:		Line 27:
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.		*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.

-	4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, or otherwise. Then:	+	4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, bad read, or otherwise. Then:

	*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect. Also, upload the sequence from the read into the wiki following the link in the rightmost column.		*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect. Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.		*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.
	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was wrong.		*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was wrong.

JCAnderson at 16:35, 4 March 2009

2009-03-04T16:35:38Z

←Older revision		Revision as of 16:35, 4 March 2009
Line 7:		Line 7:
	*On the ProgressTable google doc fill your whole line for that part in as green		*On the ProgressTable google doc fill your whole line for that part in as green
	*On the parts google doc, color the text for your part Blue to indicate that it is complete		*On the parts google doc, color the text for your part Blue to indicate that it is complete
-	*On your wiki, write in your notebook that you analyzed the ~~sequence~~ read (indicate the SBB number of the read) and note that it was correct.	+	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was correct.

JCAnderson at 16:35, 4 March 2009

2009-03-04T16:35:24Z

←Older revision		Revision as of 16:35, 4 March 2009
Line 16:		Line 16:
	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####." Also, upload the sequence from the read into the wiki following the link in the rightmost column.		*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####." Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y, change the "Part" column to your new part number..		*On the "Confirmed?" column of the StockLog page, change the ? to a Y, change the "Part" column to your new part number..
-	*On your wiki, write in your notebook that you analyzed the ~~sequence~~ read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.	+	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.


Line 24:		Line 24:
	*On the ProgressTable google doc fill your whole line for the part your really made in as green		*On the ProgressTable google doc fill your whole line for the part your really made in as green
	*On the parts google doc, color the text for the part you really made Blue to indicate that it is complete		*On the parts google doc, color the text for the part you really made Blue to indicate that it is complete
-	*On your wiki, write in your notebook that you analyzed ~~sequence~~ read (indicate the SBB number of the read) and note that it was correct but matched a different part number.	+	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was correct but matched a different part number.
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.		*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.

Line 31:		Line 31:
	*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect. Also, upload the sequence from the read into the wiki following the link in the rightmost column.		*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect. Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.		*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.
-	*On your wiki, write in your notebook that you analyzed ~~sequence~~ read (indicate the SBB number of the read) and note that it was wrong.	+	*On your wiki, write in your notebook that you analyzed the sequencing read (indicate the SBB number of the read) and note that it was wrong.

JCAnderson at 16:30, 4 March 2009

2009-03-04T16:30:56Z

JCAnderson at 16:28, 4 March 2009

2009-03-04T16:28:18Z

←Older revision		Revision as of 16:28, 4 March 2009
Line 4:		Line 4:

	*On the Sequencing page of the wiki, change the "result" section to say "perfect"		*On the Sequencing page of the wiki, change the "result" section to say "perfect"
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y.	+	*On the "Confirmed?" column of the StockLog page, change the ? to a Y.
	*On the ProgressTable google doc fill your whole line for that part in as green		*On the ProgressTable google doc fill your whole line for that part in as green
	*On the parts google doc, color the text for your part Blue to indicate that it is complete		*On the parts google doc, color the text for your part Blue to indicate that it is complete
Line 15:		Line 15:
	*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.		*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.
	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."		*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y, change the "Part" column to your new part number..	+	*On the "Confirmed?" column of the StockLog page, change the ? to a Y, change the "Part" column to your new part number..
	*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.		*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.


-	~~2) 1~~) It is a different sequence ~~from~~ our ~~assembly~~. Somehow I tube-switched my samples or got someone else's clone.	+	3) It is a different sequence that what I expected, but it matches another one of our parts. Somehow I tube-switched my samples or got someone else's clone.

	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was		*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y. Change the "Part" column to be what the clone really is	+	*On the ProgressTable google doc fill your whole line for the part your really made in as green
-	*On the ~~ProgressTable google doc fill your whole line for~~ that ~~part in as green~~	+	*On the parts google doc, color the text for the part you really made Blue to indicate that it is complete
-	*On the ~~parts google doc~~, ~~color~~ the ~~text for your part Blue~~ to ~~indicate~~ that it ~~is complete~~	+	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct but matched a different part number.
-	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was ~~correct~~.	+	*On the "Confirmed?" column of the StockLog page, change the ? to a Y. Change the "Part" column to be what the clone really is. If you think you know what the correct clone is, and it is already logged into the Stock page, color the text for that clone red and JCA will sequence that one.
		+
		+	4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, or otherwise. Then:
		+
		+	*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect
		+	*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.
		+	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was wrong.

JCAnderson at 16:21, 4 March 2009

2009-03-04T16:21:31Z

←Older revision		Revision as of 16:21, 4 March 2009
Line 3:		Line 3:
	1) It is perfect! It matches the sequence described in the StockLog google doc. There is no tube switch, there are no point mutations, all the BglBrick restriction sites are present and in the right place. It's perfect. Then:		1) It is perfect! It matches the sequence described in the StockLog google doc. There is no tube switch, there are no point mutations, all the BglBrick restriction sites are present and in the right place. It's perfect. Then:

-	*On the Sequencing page of the wiki, change the "result" section to say "perfect"	+	*On the Sequencing page of the wiki, change the "result" section to say "perfect"
-		+	*On the "Confirmed?" column of the StockLog page, change the N to a Y.
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y.	+	*On the ProgressTable google doc fill your whole line for that part in as green
-		+	*On the parts google doc, color the text for your part Blue to indicate that it is complete
-	*On the ProgressTable google doc fill your whole line for that part in as green	+	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.
-		+
-	*On the parts google doc, color the text for your part Blue to indicate that it is complete	+
-		+
-	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.	+


	2) It is almost perfect--there were some point mutations. Check and see if those point mutations are silent. If they are silent, let's go with it. Make sure you are checking the correct frame when determining whether it is silent or not. Then:		2) It is almost perfect--there were some point mutations. Check and see if those point mutations are silent. If they are silent, let's go with it. Make sure you are checking the correct frame when determining whether it is silent or not. Then:

-	*On the ProgressTable google doc fill your whole line for that part in as green	+	*On the ProgressTable google doc fill your whole line for that part in as green
-		+	*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.
-	*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.	+	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."
-		+	*On the "Confirmed?" column of the StockLog page, change the N to a Y, change the "Part" column to your new part number..
-	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."	+	*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.
-		+
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y, change the "Part" column to your new part number..	+
-		+
-	*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.	+


	2) 1) It is a different sequence from our assembly. Somehow I tube-switched my samples or got someone else's clone.		2) 1) It is a different sequence from our assembly. Somehow I tube-switched my samples or got someone else's clone.

-	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was	+	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was
-		+	*On the "Confirmed?" column of the StockLog page, change the N to a Y. Change the "Part" column to be what the clone really is
-	*On the "Confirmed?" column of the StockLog page, change the N to a Y. Change the "Part" column to be what the clone really is	+	*On the ProgressTable google doc fill your whole line for that part in as green
-		+	*On the parts google doc, color the text for your part Blue to indicate that it is complete
-	*On the ProgressTable google doc fill your whole line for that part in as green	+	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.
-		+
-	*On the parts google doc, color the text for your part Blue to indicate that it is complete	+
-		+
-	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.	+

JCAnderson: New page: I got my sequencing data, now what? Well, analyze your sequencing data, and then follow the appropriate item below: 1) It is perfect! It matches the sequence described in the StockLog ...

2009-03-04T16:20:25Z

New page: I got my sequencing data, now what? Well, analyze your sequencing data, and then follow the appropriate item below: 1) It is perfect! It matches the sequence described in the StockLog ...

New page

I got my sequencing data, now what? Well, analyze your sequencing data, and then follow the appropriate item below:

1) It is perfect! It matches the sequence described in the StockLog google doc. There is no tube switch, there are no point mutations, all the BglBrick restriction sites are present and in the right place. It's perfect. Then:

*On the Sequencing page of the wiki, change the "result" section to say "perfect"

*On the "Confirmed?" column of the StockLog page, change the N to a Y.

*On the ProgressTable google doc fill your whole line for that part in as green

*On the parts google doc, color the text for your part Blue to indicate that it is complete

*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.

2) It is almost perfect--there were some point mutations. Check and see if those point mutations are silent. If they are silent, let's go with it. Make sure you are checking the correct frame when determining whether it is silent or not. Then:

*On the ProgressTable google doc fill your whole line for that part in as green

*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.

*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."

*On the "Confirmed?" column of the StockLog page, change the N to a Y, change the "Part" column to your new part number..

*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.

2) 1) It is a different sequence from our assembly. Somehow I tube-switched my samples or got someone else's clone.

*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was

*On the "Confirmed?" column of the StockLog page, change the N to a Y. Change the "Part" column to be what the clone really is

*On the ProgressTable google doc fill your whole line for that part in as green

*On the parts google doc, color the text for your part Blue to indicate that it is complete

*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.

←Older revision		Revision as of 16:30, 4 March 2009
Line 1:		Line 1:
-	I got my sequencing data, now what? Well, analyze your sequencing data, and then follow the appropriate item below:	+	'''I got my sequencing data, now what? Well, analyze your sequencing data, and then follow the appropriate item below:'''

	1) It is perfect! It matches the sequence described in the StockLog google doc. There is no tube switch, there are no point mutations, all the BglBrick restriction sites are present and in the right place. It's perfect. Then:		1) It is perfect! It matches the sequence described in the StockLog google doc. There is no tube switch, there are no point mutations, all the BglBrick restriction sites are present and in the right place. It's perfect. Then:

-	*On the Sequencing page of the wiki, change the "result" section to say "perfect"	+	*On the Sequencing page of the wiki, change the "result" section to say "perfect". Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y.		*On the "Confirmed?" column of the StockLog page, change the ? to a Y.
	*On the ProgressTable google doc fill your whole line for that part in as green		*On the ProgressTable google doc fill your whole line for that part in as green
	*On the parts google doc, color the text for your part Blue to indicate that it is complete		*On the parts google doc, color the text for your part Blue to indicate that it is complete
-	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was correct.	+	*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it was correct.


Line 14:		Line 14:
	*On the ProgressTable google doc fill your whole line for that part in as green		*On the ProgressTable google doc fill your whole line for that part in as green
	*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.		*On the parts google doc, duplicate the line for your part and give it the next available M number. Change the sequence of this new part to match what you got from sequencing. Color this new part blue, color the old part light blue to indicate that is has been abandoned.
-	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####."	+	*On the Sequencing page of the wiki, change the "result" section to say something like "has 2 silent points, renamed M####." Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a Y, change the "Part" column to your new part number..		*On the "Confirmed?" column of the StockLog page, change the ? to a Y, change the "Part" column to your new part number..
	*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.		*On your wiki, write in your notebook that you analyzed the sequence read (indicate the SBB number of the read) and note that it had a silent mutation so you renamed it a new part number.
Line 21:		Line 21:
	3) It is a different sequence that what I expected, but it matches another one of our parts. Somehow I tube-switched my samples or got someone else's clone.		3) It is a different sequence that what I expected, but it matches another one of our parts. Somehow I tube-switched my samples or got someone else's clone.

-	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was	+	*On the Sequencing page of the wiki, change the "result" section to say "Perfect match to M####" where M#### is what the clone really was. Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the ProgressTable google doc fill your whole line for the part your really made in as green		*On the ProgressTable google doc fill your whole line for the part your really made in as green
	*On the parts google doc, color the text for the part you really made Blue to indicate that it is complete		*On the parts google doc, color the text for the part you really made Blue to indicate that it is complete
Line 29:		Line 29:
	4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, or otherwise. Then:		4) It is wrong :-( There is a missense mutation, nonsense mutation, deletion, or otherwise. Then:

-	*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect	+	*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect. Also, upload the sequence from the read into the wiki following the link in the rightmost column.
	*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.		*On the "Confirmed?" column of the StockLog page, change the ? to a N. If there was a second clone of that part already logged into the google doc, color it red, and JCA will sequence it.
	*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was wrong.		*On your wiki, write in your notebook that you analyzed sequence read (indicate the SBB number of the read) and note that it was wrong.