biopet-basecounter

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BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.

Home https://github.com/biopet/basecounter
Versions 0.1
License MIT
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopet-basecounter

BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.

For documentation and manuals visit our github.io page: https://biopet.github.io/basecounter

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install biopet-basecounter

and update with:

conda update biopet-basecounter

Notes

biopet-basecounter is a Java program that comes with a custom wrapper shell script. By default ‘no default java option’ is set in the wrapper. The command that runs the program is ‘biopet-basecounter’. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ‘biopet-basecounter -Xms512m -Xmx1g’.

docker

A Docker container is available at https://quay.io/repository/biocontainers/biopet-basecounter.