FAQ & Howtos

How to...

Find answers to probably-already-asked questions?

Check out these Q & A sites:

• SeqAnswers
• Biostars
• Biostars Galaxy

For questions related to computing problems:

• Stack Overflow
• Ask Ubuntu
• Super User

Get the best out of quality control?

• QC Fail Sequencing

• FastQC results interpretation

Download and install the SPP peak-caller?

I've struggled with this one so I'll leave a few notes here:

• Download page can be found here, better chose version 1.11.
• SPP requires the Bioconductor library Rsamtools to be installed beforehand.
• Unix packages gcc and libboost (or equivalents) must be installed.
• You can find a few more notes here.
• Good luck!

Here's the procedure I use on Ubuntu 14.04, in this very order:

In unix shell:

# unix libraries
apt-get update
apt-get -y install r-base
apt-get -y install libboost-dev zlibc zlib1g-dev

In R shell:

# Rsamtools
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

In unix shell:

# spp
wget http://compbio.med.harvard.edu/Supplements/ChIP-seq/spp_1.11.tar.gz
sudo R CMD INSTALL spp_1.11.tar.gz

Find the exact size of genomes of model organisms?

• Link