Tips, Tricks, and Sample Scripts
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?
With the increasing use of next-generation sequencing, comes the problem of how to efficiently process massive fasta files for BLAST searches.
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.
This perl one-liner will convert a fastq file into a fasta file.
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].
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.
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.
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.