Members‎ > ‎Jan Michael C. Yap‎ > ‎

MBB 291 - Bioinformatics for Genomics and Transcriptomics

Announcements

 04 November 2017 - In preparation for our hands-on exercise later, do the following:
  1. Download the transcriptomic analysis exercise kit into the home folder of your VM.
  2. Open Terminal, type unzip "Transcriptomics Exercise Kit.zip" (including the double quotes and press Enter to unpack the contents of the exercise kit.
  3. Go inside the Transcriptomics Exercise Kit folder in Terminal.
  4. Run R (type R then press Enter). 
  5. Once the R prompt comes up, type source("tdasetup.r") then press Enter. The script will install the R packages needed for our exercises.
  6. If at any point in the installation process, R asks you to update packages, press n then Enter.



04 October 2017 - Apparently, the annual UP College Admission Test (UPCAT) weekend is slated on 20-21 October, 2017. In line with this, we will not have any classes on 21 October 2017. To compensate for the cancellation of classes, I am thus adjusting our schedules. Here are the adjustments to be made:
  • Class on 07 October will be from 9:00am - 12:30pm. We will continue with the lecture and hands-on exercise on SNP Calling for the first 2 hours, and then conduct the lecture on QTL Mapping during the last 1.5 hours of class.
  • Class on 14 October will be held in the normal duration, and will focus on the parts of the QTL Mapping lecture not covered in the previous session + hands-on exercises.
  • The sessions on Transcriptomic Data Analysis will be on 04 November and 11 November instead. Unfortunately, I realize that I also have a prior commitment that I have to fulfill on 28 October, hence we have a 2-week reprieve after the 14 October class. Use this time to finish the Problem Set and to work on your Project requirement
  • In line with the above adjustment, the release of Problem Set 5 is moved to 11 November 2017, with the deadline set to 25 November 2017.
Please be guided accordingly. See you on Saturday! :)



22 September 2017 - Due to technical concerns both with network connectivity as well as server access, I'll be cancelling our class tomorrow, 23 September 2017. We'll be holding the hands-on exercise on genome assembly next week, 30 September 2017 for the first half of the class, then proceed to the lecture on SNP Calling during the second half of the class. The release of the Problem Set 3 will also be moved to next week in view of this change in schedule. Hoping for your understanding and patience. See you on the 30th of September.



14 September 2017 - Regarding Problem Set 2, if your're having problems with running tree-puzzle on your data, use the naming convention seq_XX instead of sequence_XX (where XX is the 2-letter abbreviation for the country name, e.g. PH for Philippines) for the header section of the sequences inside the FASTA-formatted file used as input for ClustalW and tree-puzzle. I forgot that tree-puzzle has an issue with long header names. Please be guided accordingly. Sorry for the misstep, and hoping for your understanding.



25 August 2017 - Hi Guys. I'm afraid I have to cancel tomorrow's (26 August 2017) class as I am dealing with colds and cough right now. If all goes well, we'll resume classes on 02 September 2017. I have also decided to extend the deadline for Problem Set 1 from 02 September to 09 September to give you more time to work on it. I've also adjusted our schedule for the semester accordingly (see right hand side). 

For those who still are having problems running the virtual machine for the purpose of doing the Problem Set, you may use R (or R-Studio) for Windows for the R part, while for Linux CLI, you can try this online Unix terminal or you may try some of the online Linux CLI emulators listed on this site. I will get back to you for tech support once we resume classes.

Again, my sincerest apologies for this abrupt development, and I promise to take care of myself better so as to avoid future instances such as this. Hope to see you all on 02 September! :)



05 August 2017 - This is the website for the MBB 291 (Bioinformatics for Genomics and Transcriptomics) class facilitated by Jan Michael Yap. Announcements and files pertinent to the class will be posted here.


DatesTopic/Activity Materials
08/05/2017Overview
08/12/2017Introduction to Linux CLI and ScriptingLinux CLI:
Site 1
Site 2

Scripting:
Site 1
Site 2
Site 3
Sample Scripts
 08/19/2017 
 Introduction to Programming in RR:
Ebook
Site 1
Site 2
08/19/2017
09/09/2017
PROBLEM SET 1Questionnaire
09/02/2017
09/09/2017
Phylogenetic AnalysisSample Data
Clustal CLI
Tree-Puzzle Manual 
09/09/2017
09/23/2017
PROBLEM SET 2Questionnaire
Dataset
09/16/2017
09/30/2017
Sequence Assembly

09/30/2017
 10/14/2017 
PROBLEM SET 3 Questionnaire
Report Table
 10/07/2017 QTL Mapping
R/qtl Tutorials
10/14/2017
10/28/2017
 PROBLEM SET 4Questionnaire
Dataset
 10/14/2017  SNP Calling 
10/28/2017
11/11/2017
 PROBLEM SET 5Questionnaire
11/04/2017
11/11/2017
Transcriptomic Data Analysis  Differential Analysis Sample Codes and Tutorials:

Microarray:
Part 1
Part 2

RNA-seq:
Link

Gene Coexpression Tutorials:
WGCNA
11/11/2017
 11/25/2017 
PROBLEM SET 6Questionnaire
Dataset
12/02/2017PROJECT PRESENTATIONTopics+Schedule
Guidelines
  • Syllabus can be downloaded here.