Bioinformatics for Beginners – Bioconductor

26/08/2013

Bioconductor is an open source, open development toolset for analysing high-throughput genomic data. It is based on the R programming language (see last week’s post about R). Bioconductor can be used for a wide range of subjects from analysing assays, to querying databases or finding candidate binding sites for...

Bioinformatics for Beginners – R

19/08/2013

No, today is not Talk Like A Pirate Day. “R” is a statistical software (more like an environment) which was inspired by “S” and was originally developed by Robert Gentleman and Ross Ihaka. Nowadays, more than a dozen contributors are working on development and bug fixes. There are also...

Workflow Wednesdays – Part 3. Read preprocessing – Subsampling

24/07/2013

It”s often a good idea (especially for large datasets) to use a subset of the reads for some preliminary analyses. A smaller dataset can be useful for figuring out the alignment parameters or checking for alignment problems.

Workflow Wednesdays – Reference sequence – Part 2. Subsampling and statistics

10/07/2013

Extracting regions from a fasta file If you are doing targeted sequencing, it’s usually a good idea to use a relatively large reference sequence (e.g. a whole chromosome) to avoid problems caused by mismappings. It can still be very useful sometimes to use a “subset” or “subsample” of the...