Tips, Tricks, and Sample Scripts

8 - [BioPerl] A note on mining taxonomic information from GenBank.

BioPerl offers modules to easily allow taxonomic information to be mined from GenBank, but what happens when taxids are updated/deleted/merged by GenBank staff?

7 - [UNIX] Tricks for processing massive fasta files for BLAST searches.

With the increasing use of next-generation sequencing, comes the problem of how to efficiently process massive fasta files for BLAST searches.

6 - [Metagenomics] Mixed-template PCR is different than single template PCR and should be treated as such.

Just as the strategy used for single template PCRs can be optimized to account for problems such as GC-content or the presence of PCR inhibitors, so too can mixed template PCRs be optimized to account for problems like the generation of PCR artefacts.

5 - [Perl] Fastq to fasta conversion.

This perl one-liner will convert a fastq file into a fasta file.

4 - [R] Resources in [R] for environmental sequence data analysis using ordination.

There are many resources available, but they are scattered across the internet. Here is a list of useful resources related to the VEGAN and ECODIST packages in [R].

3 - [R] Create scree plots using the metaMDS function in the VEGAN package.

There does not appear to be a built-in function in VEGAN for creating scree plots. Since scree plots are useful for choosing how many dimensions should be used with the metaMDS function, reference to a sample function is provided.

2 - [R] Specify which NMDS dimensions to plot when there are more than two available.

Using the nmds function in the ECODIST package, when evaluating more than two dimensions, all possible pair-wise combinations of dimensions are shown by default when using the plot function. In this example, only two specific dimensions are chosen for plotting.

1 - [R] Create a plot legend without symbols.

Normally symbols and text are both used in a plot legend. In this example, some legend entries are simply colour coded without showing a corresponding symbol.