##Tomato Interns Bioinformatics Week

Scripts, outline, and course material for teaching tomato interns.

Week of July 29, 2013

##Outline

what is atmosphere?
starting an instance
connecting to your instance
- vnc
- ssh
idrop
- move fastq files and other files to play with
Terminal
- commands at the terminal
  - idea is to define some useful commands and then give them some tasks
  - be sure to introduce the commands that they will use in examining fastq files...
    - ls
    - cd
    - pwd
    - cp
    - mv
    - mv -i
    - mkdir
    - rm
    - rmdir
    - cat
    - head, tail
    - less
    - pico or equivalent
    - grep
      - possibly with some regex (simple!)
    - pipes
    - man
Looking at fastq files (applying was learned)
- use head, tail, etc to examine fastq files
  - examine fastq file: have students describe how they appear to be organized
- exercises with grep and wc, e.g. number of reads
- grep -c

Questions/ starting problem set:
- create a new directory in /mydata
- navigate to directory in iRods with sequence files
- how many files are in the directory?
- download your desiganated file to the new directory in /mydata
- What is the machine name that the sequences come from?
- How many lines are in the file?
- How many sequence records are in the file?
- create a new file that contains 1,000,000 records from the file you downloaded
What files do we actually get back from the sequencing facility
QualityCheck
- go through FastQC, what the differenet measures mean, etc
- Phred scores
BarcodeSplit
- new QC
Trimming / filtering
- new QC
Mapping to reference
- BWA to ITAGs
- tophat to genome
Stats for mapping:
- how many ready mapped?

IGV (MFC)
- can you find genes that appear up-regulated?
  - think about normalization
- places where the data doesn't seem to match the annotation
Sam2Counts.R (JNM)
Histograms of read counts (R) (JNM)

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