SVN stuff

This is how you create a repository (usually done by IT):

svnadmin create (repo_name)

This is how you add content to a repository:

svn import (files | folder) (repo_name) -m "initial import"

This is how you checkout the latest version of something existing in SVN into the current working directory:

svn checkout (repo_name/path)

This is how you check something into it to update the svn with a more current version:

from within the root folder when doing svn checkout (ie: /workspace/genomeQC):

svn commit -m "update to ver 1.5"

FASTQ tools

Here are my favorite FASTQ processing utils:

FASTQC:

To run a QC on your data.

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

To run in batch mode with zipped output:

java* -Xmx250m -cp <> uk.ac.bbsrc.babraham.FastQC.FastQCApplication <>

*: make sure that java is at least version 1.6

FASTX Toolkit:

Bunch of scripts for processing the fastq files and qc, but fastqc is better for qc'ing.

http://hannonlab.cshl.edu/fastx_toolkit/download.html

Illumina Technote: How Illumina Sequencing works

Here's a a PDF that describes how Illumina seqeuncing works with nice graphics:
http://www.illumina.com/documents/products/datasheets/datasheet_genomic_sequence.pdf

A copy is saved here:

http://sites.google.com/site/webhostingoffiles/Illumina_datasheet_genomic_sequence.pdf

Another great article detailing sequencing technology is saved here:

http://sites.google.com/site/webhostingoffiles/Sequencingtechnologies%E2%80%94NextGen_nrg2626.pdf