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...

Workflow Wednesdays – Reference sequence – Part 1. Indexing

03/07/2013

I’ve already written some posts about fasta files and reference sequences (about file formats and where to get reference sequences. You might remember from my first “Workflow Wednesdays” post, that I selected short reads created with the three major sequencing technologies from the same E. coli strain: strain K-12...

Bioinformatics for Beginners – File formats: Part 1. Reference sequences

24/06/2013

The most widely used file format for reference sequences is the fasta format. Both nucleotide and protein sequences can be represented in fasta format. A fasta formatted file begins with a single-line description, followed by the sequence data. The description line starts with a greater-than (“>”) symbol. In the...