Etchevers:Notebook/STRA6 in eye development/2009/06/19

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Bioinformatics 101

Managed to compile the MAQ program.

First after having installed Jaunty Jackalope Ubuntu 9.04 I had to use $ sudo alt-get install build-essentials

and I also let it install all the 100 Mb additional updates.

Then I did

$ sudo alt-get install zlib1g

(I think – I did so many things and then closed the terminal window!) because it contains zlib.h, which when I tried to do

$ ./configure

from within the maq-0.7.1 folder, it wouldn't let me do first because I was missing gcc+ and then later, the zlib.h file.

I then followed instructions on the Maq software installation page using first

$ make

and then

$ make install

Then I thought I should perhaps do the same again using “sudo” because I thought I saw “error” scrolling by. That seemed to work alright.

Downloaded all the chromosomes *.fa files from

I see today I could have got them from here ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/

but instead they were from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/

and I unzipped every one and put it into a file called ref.fasta in the folder “HumGen”. I will have to rename this thing refhg18.fasta as I see only now there is a February 2009 assembly and it is called hg19!!! the original ref.fasta for hg18 is now 2.9 Gb big. Deleted all the unpacked individual chromosome files and kept the zips for now.

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

There is surely a way to batch unzip. Concatenation has happened by typing cat chr*.fa >> ref.fasta and each file gets tagged onto the end of the increasingly large ref.fasta file. Cut is ctrl-Ins and paste is Shift-Ins.

Re-downloaded all the hg19 chromosome files.