Converting between .gff, .gtf and .bed formats

Various NGS analysis tools require various input formats. It is sometimes tricky to make free software working.
Recently, all required tools for converting between .gff, .gtf and .bed formats were incorporated into Tubingen Rätsch Lab Galaxy instance

http://galaxy.tuebingen.mpg.de/

R tips

If you are looking for R tips for beginners and advanced users there is nothing better than this:
http://pj.freefaculty.org/R/Rtips.html

or in .pdf version:
http://pj.freefaculty.org/R/Rtips.pdf

Topics include:
- exchange data between R and other programs (Excel, etc)
- create variable names on the fly
- return multiple values from a function
- scatterplot: smooth a line connecting points
- test for Normality
- multiple analysis of variance
- character encoding
- R environment in side scripts

and many more. Enjoy.

[solved] git updating directory error

Today, my collaborator in a project replaced webapp/gwt/ directory with dynamic link to war/gwt directory

In .gitignore we had only this statement:

...
webapp/gwt/* 
...

During the pull origin somebranch i got this error:

git error: Updating the following directories would lose untracked files in it:
{{yourdir}}

Solution:

rm -rf {{yourdir}}
git pull origin {{somebranch}}

and add to .gitignore the conflicting dynamic link.

Google wasn't very helpfull this time. I hope this tip will help someone in the future...

[solved] libexpat.la missing

Today I got this error:

libtool: link: cannot find the library "libexpat.la" or unhandled argument libexpat.la ubuntu

To solve this issue run in apache source directory

cd srclib/apr-util/xml/expat
./configure
# OR ./configure --prefix=/{{YOURDIR}}/apache/source/httpd-2.2.22/srclib/apr-util/xml/expat/
sudo make install
# OR make install

Remember to clean up your previous apache install after make install failed

cd {{YOURDIR}}/apache/
ls -la
rm -r bin
rm -r build
rm -r include
rm -r lib

10 papers that every bioinformatician should read

This list of top 10 papers in bioinformatics does not only consist of purely bioinformatic papers, but shows how gentle and simple bioinformatics can and should be:

1. Dudley JT, Butte AJ (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Computational Biology 5(12)
Link
"Consequently it is no surprise that many successful bioinformatics apps are written by biologists who lack formal computer science training, as they undoubtedly put scientific utility ahead of architectural elegance and completeness."

2. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295)
Link
Simple and brilliant use of ChIP-seq and RNA-seq techniques.

3. Goecks J, Nekrutenko A, Taylor J, and The Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 11(8)
Link
Bioinformatics for the masses.

4. Ameur A, Zaghlool A, Halvardson J, Wetterbom A, Gyllensten U, Cavelier L, Feuk L (2011) Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nature Structural & Molecular Biology 18
Link
Great example of getting additional features from RNA-seq data.

5. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A (2009) BioMart – biological queries made easy. BMC Genomics 10
Link
Data mart for biologists.

6. Krzywinski M, Schein J, Birol I, Jones S, Marra M (2008) Circos - an information aesthetic for comparative genomics. Genome Informatics conference
Link
Beauty of data visualization.

7. Majewski J, Ott J (2004) Distribution and characterization of regulatory elements in the human genome. Genome Research 12
Link
One of the first successful attempts to analyze genomic features at genome scale.

8. Kent WJ, Zweig AS,  Barber G, Hinrichs AS, Karolchik D (2009) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26(17)
Link
Standard formats for storing NGS-data. Fast, simple.


The list will continue...

Run process as another user in init.d script

start-stop-daemon --start --quiet --chuid $USER:$GROUP --exec $SCRIPT

Installing Cassandra on Ubuntu server

# enable add-apt-repository
sudo apt-get install python-software-properties
# add repository for java
sudo add-apt-repository ppa:ferramroberto/java
# update
sudo apt-get update
# install Sun (I hate Oracle) java
sudo apt-get install sun-java6-jdk sun-java6-plugin
# create directory for installation
sudo mkdir /opt/cassandra
# add cassandra user [set password]
sudo adduser cassandra
# change owner of istallation directory
sudo chown cassandra:cassandra /opt/cassandra/
# switch to cassandra user
su -l cassandra
# go to installation directory
cd /opt/cassandra
# download latest version (check address on cassandra.apache.org)
wget http://www.apache.net.pl//cassandra/1.0.7/apache-cassandra-1.0.7-bin.tar.gz
# untar
tar xvzf apache-cassandra-1.0.7-bin.tar.gz
# back to admin account, create cassandra var directory
logout
sudo mkdir /var/lib/cassandra/
sudo chown cassandra:cassandra /var/lib/cassandra/
sudo mkdir /var/log/cassandra/
sudo chown cassandra:cassandra /var/log/cassandra/
# switch again to cassandra user
su -l cassandra
mkdir /var/lib/cassandra/data
mkdir /var/lib/cassandra/commitlog
mkdir /var/lib/cassandra/saved_caches

Add to /etc/init.d/cassandra

start-stop-daemon --start --quiet --chuid cassandra:cassandra --exec /opt/cassandra/apache-cassandra-1.0.7/bin/cassandra