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day2.txt
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Wed, Oct 9, 2013 - Illumina; shotgun sequencing; read QC
########################################################
.. `Google doc for machine names <https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidEVPSll3VXhyQVZjRXZLT25Fb0VVX1E#gid=0>`__
Outline of day:
1. Technical challenges of homework; long-running jobs
------------------------------------------------------
Review: starting up machines; connecting with SSH or IPython Notebook.
Copy/paste and putting in complete commands.
Disconnections.
Long running jobs; using screen.
Dropbox.
Shell vs IPython Notebook.
(I will deliver videos of all of these tonight.)
2. Shotgun sequencing with Illumina
-----------------------------------
(To follow along with lecture go to http://jotwithme.com/ and enter 'titus'.)
How Illumina works.
Assumptions underlying shotgun sequencing.
How the data is delivered.
- FASTQ format (see http://en.wikipedia.org/wiki/FASTQ_format)
- Phred quality scores (see http://en.wikipedia.org/wiki/FASTQ_format#Quality)
- read length
3. Quality scores, and quality evaluation
-----------------------------------------
Discuss some FastQC results here:
http://athyra.idyll.org/~t/SRR390202_1_fastqc/fastqc_report.html
and here:
http://athyra.idyll.org/~t/SRR390202.pe.qc.fq_fastqc/fastqc_report.html
What other ways might there be to evaluate the quality of your
sequencing data? (Think about things you already know, or can
assume...?)
4. What do you do with sequencing data?
---------------------------------------
Mapping vs assembly. (This will be a continuing theme :)
5. Homework solutions
---------------------
See: `solutions <http://nbviewer.ipython.org/urls/raw.github.com/beacon-center/2013-intro-computational-science/master/notebooks/hw1-ipythonblocks-SOLUTIONS.ipynb>`__.
6. More Python
--------------
Last week was "control flow" -- for and if. This week, "data structures" --
ways of storing aggregate information.
See: `in-class notebook <http://nbviewer.ipython.org/urls/raw.github.com/beacon-center/2013-intro-computational-science/master/notebooks/class2-ipythonblocks.ipynb>`__.