As promised we scheduled some excercises to be published daily in this blog. Please check it regularly. The very first are so simple that will not require further explanations, while in the future you’ll get some more complex task to submit to the instructors to be evaluated.
Please, stay tuned clicking here to view the list.
Perl & Genomics
Bioinformatics for Genomics Course – University of Padua
Author Archives: Andrea Telatin
Lab03: Cribi Crash Course
Today we met at the Vallisneri to play with the foundamentals of Perl (slides below).
Now you have some time to practice with Perl, so if you want to start from the basics here you are a step-by-step guide.
As always remember to “appello Nome Cognome” before starting, and say “goodbye” before leaving.
PDF of Perl slidesHomeworks
Dear guys,
we are really happy as we can see your efforts and your improvements. On Friday we’ll meet in Aula M Pr at 11.30, for a comprehensive course on Perl, so remember to repeat this part at home, try changing things in the scripts…
It’s going to be a long journey!
References
We are going to place useful links to presentations and manuals found on the Internet. We’ll try keeping this up to date.
LAB02 – bourne again shell!
Today we are going to:
- Refresh some shell commands, and maybe learning new ones
- Start using bioinformatics programs, in addition to the standard Linux commands
- Meet Perl for the first time. Nice to meet you!
Read this page (to the end) before starting the practical.
Continue reading
Lab02/3: first steps with Perl
This post is a part of the second laboratory session. Please refer to the main post.
Ready to start programming? We hope so. This post will teach you the very first things 🙂
What a Perl program is
As we already said in class, a Perl program (or script, better), is a plain text file, as a FASTQ or SAM file is. It contains a set of instructions that the computer can execute. Unlike human beings, computers love repetitive tasks…
We are going to give you an actual lesson of Perl next Friday, but we think it is a good idea to make you touch it in advance.
Every programming language has:
- variables: basically they are a piece of memory that can store an information, and has a name.
- conditionals: we execute an instruction IF some condition is verified.
- loops: we execute a set of instruction as many times as needed. Example: for every sequence in a FASTA file, calculate the reverse complement and print it.
Lab02/0: First quiz
This post is a part of the second laboratory session. Please refer to the main post.
First quiz for the practical: check how much did you learn about the terminal and its commands
Lab02/2: first bioinformatics programs
This post is a part of the second laboratory session. Please refer to the main post.
Linux commands like ls and grep are just programs, but they are special because any UNIX like terminal will ship them (for free :).
Now we are going to use a Perl script and an alignment program to perform two tasks:
- simulate a whole genome shotgun
- align the reads produced from the shotgun
Continuing the first practical
This is the second part of the first computer lab.
First practical
Welcome to the first practical. During this practical you’ll learn how to master the command line and Linux as well.
Please, keep in mind that all the tools we are presenting day by day are necessary to fulfil the final assignment, so try to think about all the steps rather than rushing to the end.
Feel free to ask us, in case of troubles…