xPore v2.1

[ploy-np]

Summary

xPore v2.1 has some minor changes from the previous version, which include the following.

• All k-mers containing ‘N’ will be discarded in both options i.e. with and without --genome in xpore dataprep.
• New GFF option: to map the transcriptomic to genomic coordinates (when using --genome in xpore dataprep), xPore requires both FASTA for sequence information and either GTF or GFF for coordinate information. However, GTF is the recommended option. If GFF is the only file available, please note that the GFF file works with GENCODE or ENSEMBL FASTA files, but not UCSC FASTA files. We plan to remove the requirement of FASTA files in a future release.
• In xpore dataprep, the option names have been changed as follows.
  • --gtf_path_or_url to --gtf_or_gff
  • --transcript_fasta_paths_or_urls to --transcript_fasta
• The link to our demo dataset in zenodo was corrected.
• The documentation was updated to include these changes.

What's Changed

• gtf option, fastdataprep, and dataprep intermediate file removal by @yuukiiwa in gtf option, fastdataprep, and dataprep intermediate file removal #48
• Update README.md by @jonathangoeke in Update README.md #49
• remove pyensembl requirement and solve Arabidopsis bug by @yuukiiwa in remove pyensembl requirement and solve Arabidopsis bug #57
• Update README.md by @jonathangoeke in Update README.md #51
• replace if statement with KeyError in g2t mapping, add post-processing option, and add xpore wrapper by @yuukiiwa in replace if statement with KeyError in g2t mapping, add post-processing option, and add xpore wrapper #58
• Update README.md by @jonathangoeke in Update README.md #66
• Update help.rst by @jonathangoeke in Update help.rst #67
• readGTF function was modified to adapt to non-ensembl GTF input by @obenno in readGTF function was modified to adapt to non-ensembl GTF input #87
• add assert "NNNNN" for process_tx and solve bug with stringtie gtf by @yuukiiwa in add assert "NNNNN" for process_tx and solve bug with stringtie gtf #96
• Fix quickstart doc by @hendrikweisser in Fix quickstart doc #103
• Add GFF annotation option and change fasta and gtf input flags names by @yuukiiwa in Add GFF annotation option and change fasta and gtf input flags names #90
• update readthedocs with --gtf_or_gff specifics by @yuukiiwa in update readthedocs with --gtf_or_gff specifics #105

New Contributors

• @yuukiiwa made their first contribution in gtf option, fastdataprep, and dataprep intermediate file removal #48
• @jonathangoeke made their first contribution in Update README.md #49
• @obenno made their first contribution in readGTF function was modified to adapt to non-ensembl GTF input #87
• @hendrikweisser made their first contribution in Fix quickstart doc #103

Full Changelog: v0.5.6...v2.1

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This discussion was created from the release Bugs fixed and GFF feature added.