Bioinformatica: introduzione (BMR Genomics) - Lezione 25 luglio 2014
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Transcript of Bioinformatica: introduzione (BMR Genomics) - Lezione 25 luglio 2014
Bioinformatics TrainingIntroduction to Perl Programming
Andrea Telatin
Andrea TelatinBecoming a Bioinformatician
We started with…
1. Most bioinformatics file formats are text files!
2. There are quite a few robust programs
3. Our goal is often to create a pipeline
4. For most pipelines we need some glue
Re-loading…
Re-loading…
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
Playing with the BASH
• Example 1:
• Download 3 to 5 PNG images from the web
• Install the program “ImageMagik” using the repository (apt-get…)
BASH COMMANDS
BIO TOOLS
Andrea TelatinBecoming a Bioinformatician
Playing with the BASH
• Move to the download images directory
• Type “convert -resize 50% image1.png small1.png”
• How to automate the process to create a smaller version of all the images?
BASH COMMANDS
BIO TOOLS
Andrea TelatinBecoming a Bioinformatician
Playing with the BASH
• Remember of the “man command”
• Never forget about google
BASH COMMANDS
BIO TOOLS
Andrea TelatinBecoming a Bioinformatician
Playing with the BASH• Now you should create a directory for today’s tasks
• Then download into it (using wget):
• http://www.telatin.com/reads.tar.gz
• http://www.telatin.com/amplicon.tar.gz
• The human chromosome 2 (hg19)
BASH COMMANDS
BIO TOOLS
Andrea TelatinBecoming a Bioinformatician
Reads alignments• Extract the .tar.gz archives using tar. Check via
google how to do this (tar is a strange program)
• Now we have to install bwa to align reads. We can use the repository again.
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
Reads alignments• Create an index: bwa index genome.fa
• Align reads: bwa mem genome.fa reads.fastq > output.sam
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
SAMtools• Download them via the repository
• SAM to BAM pipeline: • samtools view -bS file.sam > file.bam • samtools sort file.bam sorted_file • samtools index sorted_file.bam
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
IGV• DON’T Download it via the repository. Download it
from the internet!
• Unzip it into a directory (eg: IGV in your home)
• Launch it with the terminal: “sh igv.sh”
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
IGV
• Load as genome the human chromosome 2
• Load as tracks both the BED and the BAM files
BASH COMMANDS
BIO TOOLS
PERL
Andrea TelatinBecoming a Bioinformatician
BASH COMMANDS
BIO TOOLS
PERL
BED/GFF
VCF
BAM
Programming:an introduction
BASH COMMANDS
BIO TOOLS
PERL
INPUT (files, parameters) ELABORATION (steps to transform the input) !OUTPUT (files, text…)
INPUT (files, parameters) ELABORATION (steps to transform the input) !OUTPUT (files, text…)
Try thinking about “grep” or “head”
Imitare i programmi della shell è un buon modo per farne!di validi.!I programmi della shell:
• Hanno una guida (documentazione) • Hanno dei comportamenti standardizzati (si imparano
in fretta una volta imparati questi standard) • Sono robusti (controllano l’input, danno errori che ci
aiutano a lanciarli correttamente)
Programmare significa saper scomporre il !nostro obiettivo in passaggi !che un computer possa effettuare.
Programming:a live introduction
http://www.codepad.org/
Possiamo usare per le piccole “prove” un sistema online per interpretare codice Perl