In the practical class of this module students will mostly work in
groups and carry out the tasks proposed in the lab guides that will be
rendered available. Discussion on the answers will be performed by the
groups in collaboration with the professor. Students are advised to take
contact with the lab guide and with the softwares before the class so
that the discussion can be profitable. More specific comments to each
lab class are provided below.
Lab T0 (week 1)
For this lab students will use the lab guide and also the example sequences provided, nucleotides and amino acids.
Lab T1 (weeks 2 and 3)
For this class students will make use of a software called CLC Genomics Workbench
that you can find simply by googling its name. To access this software
you can ask for a trial license to use and use it in your own
desktops/laptops. It would be perfect if all students already had the
software downloaded for the practical classes next week where we will
approach the assembly of genomes. It is possible that some command lines
are different in the lab guide (because your version is newer),
however, if you find difficulties while doing the protocol let me know
and i'll try to figure them out.
Notes for Lab 1 :
- All groups use for part 1 Q5 and for part 2 the DNA sequences (contigs) that have been assigned in class. You have that info in the files "Distribution of contigs".
- To help conclude part 2, you have available a file similar to the one I have shown in the theoretical class (it is named support to gene finding"
- To get the most of points for part 2, please make sure that you discuss 4 differences between the predictions made by GeneMarkS or Augustus. In case your assigned DNA sequence does not give you these many differences, try to expand the region you are analyzing by an extra 10,000 nucleotides (e.g. you are examining a region between 1-20,000 and to obtain more differences you expand to go from 1-30,000);
- While making the BLASTP of your Augustus-predicted proteins make sure you copy just the aminoacids but not the # or the spaces because that affects the result.
Lab T2 (transcriptomics)