Deep Sequencing Notes
The solexa pipeline converts images to fragment sequences. Beware that the space requirements are probabhly larger than you expect:
Each lane is measured individually and placed in a folder L00<lane>
In each folder we have the different cycles called C<cycle>.1
In each cycle we have around 330 scanned tiles listed as s_<lane><tile><base>.tif
Each image is 2Mb, so in total we have
2Mb * 4 (bases) * 330 (tiles) * 8 (lanes) * 36 (cycles) = 760320 Mb = 742 Gb
The paired end module might potentially double this to 1.45 Tb per experiment.
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FFTW seems to be at version 2.1.5 on the standard install and that does not work.
Download fftw 3.1.2.tar.gz from
Unyip it and go to the direcrtory fftw-3.1.2
Enter ./configure --enable-float
sudo make install
which will install the fftw3 package in /usr/local/lib/
Add the line
LDFLAGS += -L/usr/local/lib/
at the top of
apt-get install gnuplot apt-get install libbz2-dev (the bzlib library and headers) apt-get install libxml-simple-perl (this is the XML::Simple perl module) apt-get install imagemagick (provides convert)
To then compile the software you should remove the dependecy files and object files in the firecrest/Matrix directory. Practically this is done with rm *.d *.o
Don't forget to type make install, otherwise the goat directory will be missing a lot of useful executables.
Also not that the goat folder should be pointing to some of the proper binaries and those links need to be made manually:
cd Goat ln -s ../Firecrest/run_image_analysis . ln -s ../Firecrest/analyse_image . ln -s ../Bustard/run_base_caller . cd Matrix ln -s ../../Firecrest/Matrix/savinio . cd ../Phasing ln -s ../../Bustard/Phasing/phasing_estimate .