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processTerminalExons(features, min_overhang = NA)TxFeatures objectNA to
exclude all terminal exons sharing a splice with an internal exon
and trim all remaining terminal exons overlapping other exons.TxFeatures object with processed features
predictTxFeatures predicts flanking terminal exons for each
identified splice junction. This ensures that each splice junction
has a flanking exon after merging with mergeTxFeatures.
This approach results in many predicted terminal exons that
share a splice site with predicted internal exons (often contained
within them or with a short overhang due to incorrect alignments).
Most of these are not real terminal exons and are filtered before
further analysis. Filtering based on the overhang is controlled with
argument min_overhang.
Some of the remaining predicted terminal exons overlap other exons
such that their unspliced boundary shows a short overhang with
respect to a spliced boundary of the overlapping exon. Often these
exon extensions into an intron are due to incorrect alignments.
Terminal exons with overhang smaller than min_overhang are
trimmed such that their trimmmed unspliced boundary coincides with
the spliced boundary of the overlapping exon.
txf_processed <- processTerminalExons(txf_ann)
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