Difference between revisions of "Talk:Chlamydia trachomatis"

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(GenMAPP User Notes: fixed link syntax)
(gave feedback on week 13 status)
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== Week 13 Feedback ==
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* The IDs of the form pCTA_#### probably come from a plasmid and should be kept.  I'm glad that changing the regular expression in match to capture these then gave a count that matched what was in the OrderedLocusNames table in Access.
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* You will need to talk with Dr. Dionisio to find out why the SQL query and the TallyEngine gave a different number and what the fix will be.
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* Your assumption about the "suffix" added to the IDs in the microarray data is correct.  Excel has a function "Text-to-columns" that will allow you to separate the suffix off so that you just have the IDs that you want.  I can show you this in class on Tuesday.  ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:13, 25 November 2013 (PST)''
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== GenMAPP User Notes ==
 
== GenMAPP User Notes ==
  

Revision as of 00:13, 26 November 2013

Contents

Week 13 Feedback

  • The IDs of the form pCTA_#### probably come from a plasmid and should be kept. I'm glad that changing the regular expression in match to capture these then gave a count that matched what was in the OrderedLocusNames table in Access.
  • You will need to talk with Dr. Dionisio to find out why the SQL query and the TallyEngine gave a different number and what the fix will be.
  • Your assumption about the "suffix" added to the IDs in the microarray data is correct. Excel has a function "Text-to-columns" that will allow you to separate the suffix off so that you just have the IDs that you want. I can show you this in class on Tuesday. Kdahlquist (talk) 16:13, 25 November 2013 (PST)

GenMAPP User Notes

Week 10 Feedback

  • Thank you for submitting your team page on time.
  • We are expecting roughly equal contributions from all team members; Dillon only made a few saves compared to Katrina and Hilda.
  • As for the construction of your team page, you have only provided links to the User pages for your team. There are some additional useful links that you could provide for your team's page, what should they be?
    • We encourage you to create a template for your team's useful links.
  • The full bibliographic reference needs to be provided for microarray reference 1.
  • You have only provided links to the HTML versions of the papers; please provide direct links to the PDF downloads for these articles.
  • Microarray reference one is approved for your project (you can comment out the references to the other microarray papers so that they don't appear on the page). You will need to talk to me in class to discuss how to proceed with the data.

Kdahlquist (talk) 14:41, 4 November 2013 (PST)

Additional Week 10 Notes

  • As I mentioned to you in class today, the strain of Chlamydia from which the IDs on the microarray are taken (Olmsland et al. paper) is a different strain than the reference strain for which you found your original genome paper.
    • The reference strain is: Chlamydia trachomatis (strain D/UW-3/Cx) with a taxonomic ID of 272561.
    • The strain used for the gene IDs on the chip is: Chlamydia trachomatis serovar A (strain HAR-13 / ATCC VR-571B) with a taxonomic ID of 305277.
  • You may choose to do your journal club on either strain, but for your project to work, you need to match the UniProt and GOA downloads with the microarray chip IDs.

Kdahlquist (talk) 16:27, 5 November 2013 (PST)

File Naming Convention

Please use the following format in naming all of the files that you work with <Descriptive term(s)>_v<version number>_<Initials>_<yyyymmdd>

  • For example: UniProt_v1_KS_201312107

Ksherbina (talk) 09:44, 7 November 2013 (PST)

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