Wed, Oct 2, 2013 - ipythonblocks; read QC

Google doc for machine names

Outline of day:

0. Survey.

(until ~20 minutes after)

You should all have received a survey e-mail from Claudia Vergara. Please fill out survey; I will leave room and return at 20 after.

1. Introduction; office hours; grading and hand-in policy.

I’ve already done the introduction at the workshops, but basically we’re going to show you three things in this class: (1) some basic programming, (2) how to run and think about sequence data analysis, and (3) how to do some simple evolutionary modeling.


There will be some online lectures, especially about technical stuff like starting up machines, handing in homework, and various aspects of programming and running NGS programs.

Homework and grading

If you’re auditing you’re expected to hand in the homeworks until you stop auditing, and vice versa.

Grading will be P/F each week, with each week representing 10% of the final grade.

Homework handed in after the official due date/time may not be graded.

If I do not send you comments on your homework by the end of the weekend following hand-in, (Sunday evening), you get a PASS garde.

I would suggest that you get together in study groups to do the homework.

Office hours

Primary support will be via e-mail. I can schedule a Google Hangout with you if you need one-on-one or one-on-group time. I propose to specify one or two times a week where I will be available, decided on by Doodle polls. Pushback?

2. ipythonblocks introduction; in-class exercises.

Pick one of the machines randomly (see Google doc for machine names) and open up a new IPython Notebook link. (Password: ‘beacon’.)

Select the notebook ‘class1-ipythonblocks’ & make a copy!

See a static copy of the notebook here.

3. Read trimming and QC; FastQC reports.

A short introduction to NGS sequencing, and what can go wrong; a FastQC report. (Lecture whiteboard: go to JotWithMe/titus801-1.)

To see a FastQC report, pick one of the machines randomly (see Google doc for machine names) and open up the associated FastQC link. To generate this, I did

cd /usr/local/share
curl -O
chmod +x FastQC/fastqc

cd /root
curl -O
curl -O

mkdir /var/www/fastqc
/usr/local/share/FastQC/fastqc 100k_1.fq 100k_2.fq -o /var/www/fastqc