This is the test repository for TENNIS, a tool to identify missing transcripts from transcriptome annotations.
Scripts and documentation for test purposes are available in the analyses directory.
Software programs should be installed and softlinked in programs dir. For example, TENNIS should be installed and softlinked to programs/tennis.py.
cvbio is needed to convert chromosome names between different annotations. It should be softlinked to programs/cvbio.
More detailed descriptions can be found in programs/install.md
The following transcriptome annotations were used in experiments. They need to be downloaded to data dir and named to the corresponding name, e.g. data/dm6.gtf. More about data.
| Species | Annotation |
|---|---|
| Human | GENCODE-GRCh38 |
| Human | RefSeq-GRCh38 |
| Mouse | GRCm39 |
| Drosophila | dm6 |
| Zebrafish | GRCz11 |
| Maize | Zm-B73-REFERENCE-NAM-5.0 |
| Arabdopsis | TAIR10 |
Scripts and documentation for test purposes are available in the analyses directory.
Section 3.1 is reproducible using analyze_annotations.ipynb
Section 3.2 is reproducible using long_read_support.ipynb
Section 3.3 is reproducible using pred_removed_isoforms.ipynb