junction-annotation
The junction-annotation command will search an RNA-Seq bam file for splice junctions, compare them to a gene model, and output whether the found junctions are novel, partially novel, or already annotated in a gene model. In addition to a summary of the junctions and spliced reads, per-junction annotations are output with their location and number of supporting reads.
CompleteNovel: Neither the 5' splice site or the 3' splice site are in the gene model PartialNovel: Only one of the 5' splice site or the 3' splice site are in the gene model Known/Annotated: Both the 5' splice site and the 3' splice site are in the gene model UnannotatedReference: The contig on which the splice was discovered is not in the gene model. Nothing can be stated about the known or novel status of this splice.
The following criteria are adjustable for junction detection and read filtering:
| Option | Help |
|---|---|
-i, --min-intron |
Minimum intron length to be considered a junction (default: 50) |
-q, --min-mapq |
Minimum read quality to be considered a supporting read (default: 30) |
-m, --min-reads |
Minimum number of reads supporting a junction for it to be reported (default: 2) |
-k, --fuzzy-junction-match-range |
Consider exonic starts/ends within +-k bases of a known intron start/end to be known (default: 0) |
-c, --consider-unannotated-references-novel |
For the summary report, consider all events on unannotated reference sequences complete_novel. Default is to exclude them from the summary. Either way, they will be annotated as unannotated_reference in the junctions file. (default: False) |
In the resulting <basename>.junctions.tsv files, note that the coordinates are 0-based, end-exclusive. Generation of these files can be disabled with --disable-junction-files. Instead only the summary of junction and splice counts will be generated.