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.
BaseCounter requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.
Download the latest version of BaseCounter here. To generate the usage run:
java -jar <BaseCounter_jar> --help
BaseCounter takes a refflat file and a bam file. Also an output directory needs to be specified. Optionally a prefix for the output files can be specified.
This tool produces a number of tab-seperated output files in the specified output directory. Each of these files contains the base counts for a different type of feature (exon, intron, gene, transcript or meta-exon) or a different strandedness (normal, sense or anti-sense).
For the gene and transcript output an "exonic" and "intronic" output is also generated. These contain the counts for only the exonic regions of a gene/transcript and only the intronic counts for a gene/transcript.
For the exon and intron output a "merge" output is also generated. In these files the counts are given, in which overlapping exons within a gene are considered one exon.
Meta-exons are the exons split into separate features based on the overlap of exons between transcripts and genes.
To count the bases in
bamfile.bam usin the regions specified by
java -jar <BaseCounter_jar> \ -r refflatfile.refflat \ -b bamfile.bam \ -o output_dir \ -p prefix
Usage for BaseCounter:
|Option||Required||Can occur multiple times||Description|
|--log_level, -l||no||no||Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'|
|--help, -h||no||no||Print usage|
|--version, -v||no||no||Print version|
|--refFlat, -r||yes||no||refFlat file. Mandatory|
|--outputDir, -o||yes||no||Output directory. Mandatory|
|--bam, -b||yes||no||Bam file. Mandatory|
|--prefix, -p||no||no||The prefix for the output files|
BaseCounter is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.
BaseCounter is build using sbt. Before submitting a pull request, make sure all tests can be passed by
sbt test from the project's root. We recommend using an IDE to work on BaseCounter. We have had
good results with this IDE.