Category: computer lab

Today you're going to take a "self serve" lab. Skim this post and decide where to focus (no particular order suggested/required). We recommend to review thing you found difficult/no clear. For technical aspects feel always free to ask us. We suggest to dedicate at least some time, if not the whole afternoon, to riboclass data analysis. If you need to write notes, create a day4.txt in the dir-01 directory :) (more…)

Submit a job to CAMERA You'll find in your home folder a new directory called "files". Inside it we put a random selection of reads from both RNA-Seq and WGS (called like rrna.geno-XX.fasta and gdna.geno-XX.fasta). Submit both to CAMERA using a proper analysis. A look at our outputs We launched a BLAST alignment of short reads against a 16S ribosomal database (using -m 8 for tabular output), and we did the same using PASS (asking for SAM output). You will find both outputs in the "files" directory, in your home. Today we'll play with pass_output.sam from PASS. (more…)

Time has come to perform a BLAST from the command line, finally. This enable you using thousand if not billions of sequences as query, and to use a custom database as a reference. Your goals are to set up a local BLAST and test it, and to prepare the command to BLAST all the metagenomics sequences produced by the Ion Proton against the proper database. (more…)

Today will start using the Linux shell: a command line interface to launch programs. Our goals are: 1) Getting familiar with Ubuntu 2) Start typing commands in a terminal 3) Understanding simple text files and their importance in bioinformatics This is the first time we use the computer room. Please, skim the whole instructions post before starting. Then take some time (at least 1h) to work alone. Remember that Google is your friend. See the Computer Lab page for general hints. (more…)