RefflatStats generates stats about an annotation refflat file. It outputs stats files on genes, transcripts, exons and introns. Information includes start,end information, GC content, number of exonic regions etc.
RefflatStats 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 RefflatStats here. To generate the usage run:
java -jar <RefflatStats_jar> --help
RefflatStats requires the refflat file and an indexed reference fasta to run.
If the reference is in reference.fa
then a reference.fai
and a
reference.dict
must also be present.
To output information on genes, transcripts, exons and introns:
java -jar <RefflatStats_jar> \
-a MouseAnnotation.refflat \
-R IndexedMouseReference.fa \
-g GeneOutput.tsv \
-t TranscriptOutput.tsv \
-e ExonOutput.tsv \
-i IntronOutput.tsv
Usage for RefflatStats:
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 |
--annotationRefflat, -a | yes | no | The refflat file used for annotation |
--referenceFasta, -R | yes | no | The reference fasta file |
--geneOutput, -g | yes | no | Ouput file for genes |
--transcriptOutput, -t | yes | no | Output file for transcripts |
--exonOutput, -e | yes | no | Output file for exons |
--intronOutput, -i | yes | no | Output file for introns |
RefflatStats 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.
All tools in the BIOPET tool suite are Free/Libre and Open Source Software.
The source code of RefflatStats can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.
RefflatStats is build using sbt. Before submitting a pull request, make sure all tests can be passed by
running sbt test
from the project's root. We recommend using an IDE to work on RefflatStats. We have had
good results with this IDE.
For any question related to RefflatStats, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.