Chipster_genomes
Chipster_genomes is a help tool to download genome indexes used in Chipster software to Puhti. CSC is maintaining several short read aligners (e.g. BWA, Bowtie2, STAR) in Puhti, but not the pre-calculated indexes for reference genomes. By default, users need to import and index themselves the reference genomes they are using.
The Chipster server, however, contains indexes for a set of commonly used reference organisms for several aligners.
The genome data and indexes used in Chipster are based on the data available in Ensembl and Ensembl genomes databases. However, in Chipster, only those sequences (chromosomes) that have been assigned to a karyotype, are included. Further, in GTF files negative location values are removed.
Thus, the data downloaded from Chipster server may, in some cases, differ from the data obtained directly from Ensembl.
License
Free to use and open source.
Available
Available in Puhti.
Usage
The chipster_genomes tool is included in the biokit module, so to make it available, you must first run the set-up command:
module load biokit
After that, you can use chipster_genomes command. This command needs two parameters:
- File or index type (bed, gtf, fasta, bowtie, bowtie2, BWA, Hisat2, TopHat2)
- Species name
If the command is launched without any arguments, it first lists the available data types and asks to select one of them. Then the species available for the given datatype are listed, and the tool asks the user to select one of them.
chipster_genomes
The data type can, alternatively, be given as the first argument and the species name as the second argument. For example, the BWA indexes of Danio_rerio.GRCz11 can be retrieved with the command:
chipster_genomes bwa Danio_rerio.GRCz11
Note that as the index files may be rather large, you should normally download the data to your /scratch disk area.