What's Changed
The workflow has changed substantially since v0.1.0 and is now as follows:
- Use StringTie to assemble transcripts from aligned RNA-seq reads
Filter assembled transcripts for minimum mean expression across samples of the same condition (Biorxiv, Swamy et al., 2020) - Filter for novel last exons that extend a known exon (optionally checking that the 5'ends match) or contain a novel last splice junction (optionally checking that the novel 5'ss matches a known 5'ss)
- Filter assembled transcripts for last exons with nearby reference polyA site (e.g. PolyASite) or conserved polyA signal motif (e.g. 18 defined in Gruber et al., 2016)
- Merge novel last exon isoforms with reference annotation, quantify transcripts with Salmon
- Output count/TPM matrices via tximport for use with downstream differential transcript usage packages
- Perform differential usage analysis between two conditions using DEXSeq
Other updates:
- Extensive documentation update
- Added license
- Addition of simulated test data
- sge profile removed (it was never working in the first place)
The relevant PRs can be found here:
- Script to filter GTF file based on attributes by @SamBryce-Smith in #29
- v0.2.0 by @SamBryce-Smith in #39
Full Changelog: v0.1.0...v0.2.0
Contributors
SamBryce-Smith