A simple .sh script to annotate circRNA/backsplice junctions based on GENCODE annotations (for now).
sh annotate.sh candidate_circRNA.bed gencode.v39.annotation.gtf
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BEDTools (tested on v2.30.0)
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GENCODE annotation file in GTF format (ungzipped)
List of circRNAs in BED6 format
| Chromosome | Junction start | Junction end | circRNA ID | score (ignored) | Strand |
|---|
Example input
1 100049908 100080659 1:100049908-100080659:+ . +
"annotatedCircs.txt"
| Column | Description |
|---|---|
| 1 | Chromosome |
| 2 | Junction start |
| 3 | Junction end |
| 4 | circRNA ID (chr:start-end:strand) |
| 5 | Strand |
| 6 | Type (exon, intron, intergenic) |
| 7 | Host gene ensembl ID (N/A if intergenic) |
| 8 | Gene biotype |
Example output
chr1 100049908 100080659 1:100049908-100080659:+ + exon ENSG00000283761.1 protein_coding
chr1 100049908 100080659 1:100049908-100080659:+ + exon ENSG00000156875.14 protein_coding
If coordinates overlap with multiple features, they will all be listed in the output.