Difference between revisions of "DiffKAP"
| Line 7: | Line 7: | ||
== What does DiffKAP depend on? == | == What does DiffKAP depend on? == | ||
DiffKAP depends on the following things: | DiffKAP depends on the following things: | ||
| − | * | + | * [http://www.cbcb.umd.edu/software/jellyfish jellyfish] for fast kmer counting |
| − | + | * blastx for sequence alignment | |
| + | * Some non-standard Perl modules: | ||
| + | ** bioperl | ||
| + | *** Bio::SeqIO | ||
| + | *** Bio::SearchIO | ||
| + | ** Parallel::ForkManager | ||
| + | ** Statistics::Descriptive | ||
| + | ** Config::IniFiles | ||
Revision as of 01:55, 23 November 2011
We have developed a Differential kmer Analysis Pipeline (DiffKAP) for the pairwise comparison of RNA profiles between metatranscriptomes which does not rely on mapping to reference assemblies. By reducing each read to component kmers and assessing the frequency of these sequences, we overcome statistical limitations on the lack of identical reads for pairwise comparison between samples and allow inference of differential gene expression for annotated reads.
The DiffKAP application consists of a series of scripts written in Perl and Linux shell scripts and requires Jellyfish [Marcais 2011] and BLASTx as well as access to a copy of the SwissProt database. The scripts are freely available for non-commercial use.
What does DiffKAP depend on?
DiffKAP depends on the following things:
- jellyfish for fast kmer counting
- blastx for sequence alignment
- Some non-standard Perl modules:
- bioperl
- Bio::SeqIO
- Bio::SearchIO
- Parallel::ForkManager
- Statistics::Descriptive
- Config::IniFiles
- bioperl
How to install
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