Template:SBB-Protocols SeqResult

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Current revision (12:37, 4 March 2009) (view source)
 
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I got my sequencing data, now what?  Well, analyze your sequencing data, and then follow the appropriate item below:
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'''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:
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*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
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*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 sequencing read (indicate the SBB number of the read) and note that it was correct.
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*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.
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*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 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.
-
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
+
*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
-
*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.
-
4)  It is wrong :-(  There is a missense mutation, nonsense mutation, deletion, or otherwise.  Then:
 
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*On the Sequencing page of the wiki, change the "result" section to say "Wrong--has deletion" or something to that effect
+
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 "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.

Current revision

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". 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 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 the sequencing 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####." 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 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.


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 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 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.


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 "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.
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