some-exercises.txt

Some exercises to try
=====================

0. Finish or re-run one of the tutorials that you're particularly interested
   in.

1. Download and assemble some reads from the Short Read Archive (SRA)
   or elsewhere.

   Remember that `the ENA at EBI <http://www.ebi.ac.uk/ena/>`__ offers
   FASTQ downloads of SRA sequence.

   (see these tutorials: :doc:`reads_and_qc` and `assembly-lab`)

2. Browse the `NCBI Bacterial genomes site
   <http://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/>`__, download a proteome
   of interest (you'll want the '.faa' files), and run the various BLASTs
   on 'em (e.g. find reciprocal best hits).

   See the instructions here: :doc:`tuesday`.

3. Map raw reads for the E. coli 0104 genome back to your assembly --
   e.g. take the assembly at http://athyra.idyll.org/~t/ecoli-v41.fa
   and map the QC reads to it (see :doc:`bwa_mapping`).

   Bonus: load the resulting read mapping into Tablet.

   Bonus x 2: use the Prokka annotation .gff file to define features
   in Tablet.  (If you didn't get all the way through the Prokka run,
   you can download a zip file of the results here:
   http://athyra.idyll.org/~t/ecoli0104-prokka.zip)

4. Assemble the provided ecoli reads *without* digital normalization.

5. Install BLAST and the ngs-scripts, and then try comparing an assembly
   with a genome by using the following commands::

      blastall -i assembly.fa -d genome.fa -p blastn -e 1e-20 -o assembly.x.genome.blastn
      blastall -d assembly.fa -i genome.fa -p blastn -e 1e-20 -o genome.x.assembly.blastn

      python /usr/local/share/ngs-scripts/blast/calc-blast-cover.py genome.fa assembly.x.genome.blastn 300 assembly.fa
      python /usr/local/share/ngs-scripts/blast/calc-blast-cover.py assembly.fa genome.x.assembly.blastn 300 genome.fa

6. Try taking one of the assemblies
   (e.g. http://athyra.idyll.org/~t/ecoli-v41.fa) and mapping the QC
   reads used to assemble it back to it, to assess assembly completeness.