Template:SBB-Protocols SeqResult

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(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 ...)
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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.
+

Revision as of 12:21, 4 March 2009

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.
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