There is a huge mess in the fastq format description and sometimes you might get lost trying to find which is the encoding of your file. Because of that i found a script written in here https://github.com/brentp/bio-playground/blob/master/reads-utils/guess-encoding.py that you can use to find out which is the correct version of your files with the command:

awk ‘NR % 4 == 0’ your.fastq | python %prog [options]

So far this support the following encodings:

‘Sanger’: (33, 73),
‘Solexa’: (59, 104),
‘Illumina-1.3’: (64, 104),
‘Illumina-1.5’: (67, 104)
My file outputed Solexa  Illumina-1.3    (66, 104)
There is also this script:
./SolexaQA.pl reads1.fastq

Related Posts

Relatório de Atividades LGC

Sobre o futuro da publicação científica

http://the-scientist.com/2012/08/01/whither-science-publishing/ Related PostsReport 21/09/12Fastq – Guessing between 4 formatsLibraries to generate plot for BioinformaticsReport 02/10/12How to test speed from internet using the command line ?Cluster Commands and Tricks 06/09/11

Relatório de Atividades LGC

Mudando atalhos no Sublime Text 2

Edição do arquivo Default(linux).sublime-keymap { “keys”: [“ctrl+d”], “command”: “toggle_comment”, “args”: { “block”: false } }, { “keys”: [“ctrl+shift+d”], “command”: “toggle_comment”, “args”: { “block”: true } }, Source:http://stackoverflow.com/questions/11598840/keyboard-shortcut-to-comment-lines-in-sublime-text-2 Related PostsReport 210213Less without WordWrapCluster Commands and Tricks Read more…

Relatório de Atividades LGC

Mendeley sharing papers across computers

Goal: Organize all your papers and being able to use Mendeley from home and at work for this task. First Problem: Since I’ve being using different computers for saving my articles I first had to Read more…