feature prediction other than protein coding genes

[CeciliaDeng]

Description of feature

Dear genePal team,

The pipeline used to predict features like snoRNA, rRNA, miRNA, tRNA, three- and five-prime UTRs etc.

With v0.6.0, all these features were not there anymore. According to the CHANGELOG, rRNA and tRNA were removed in v0.5.0. Is it possible to keep predictions of all those non-protein-coding features and attach them to the gt.gff3 file after the 'downstream' work?

Thank you very much.

[GallVp]

Thank you for the issue. These features are not predicted by BRAKER which only predicts protein coding genes. In the earlier versions, these features were allowed in the liftoff sub-workflow. That was a mistake as the pipeline did not know how to handle these features in the downstream tools such as eggnog-mapper. Therefore, for the time being, the liftoff of these features has been turned off. On 28 Jan 2025, at 11:53 AM, Cecilia Deng ***@***.***> wrote: Description of feature Dear genePal team, The pipeline used to predict features like snoRNA, rRNA, miRNA, tRNA, three- and five-prime UTRs etc. With v0.6.0, all these features were not there anymore. According to the CHANGELOG<https://checkpoint.url-protection.com/v1/r01/url?o=https%3A//github.com/Plant-Food-Research-Open/genepal/blob/main/CHANGELOG.md&g=OGJjZWJhNjhiNzM1N2QxMg==&h=MTgxMTJjNDE2MmYzMmMxNmQ5ZmNlMDNhMDA0NmRlMjZmNTY5MWQ5OWFjOWViODBmMzkyM2E4NzNhZGQ4NmQ5NA==&p=YzJ1OnBsYW50YW5kZm9vZHJlc2VhcmNoOmM6bzoxYzczZGRhOWQ5NDRjOTQzZjU1YjkyNzg2YWViNTlkMjo3Omg6VA==>, rRNA and tRNA were removed in v0.5.0. Is it possible to keep predictions of all those non-protein-coding features and attach them to the gt.gff3 file after the 'downstream' work? Thank you very much. — Reply to this email directly, view it on GitHub<https://checkpoint.url-protection.com/v1/r01/url?o=https%3A//github.com/Plant-Food-Research-Open/genepal/issues/134&g=Y2IzY2U3YTQ5N2Q4MDg0MA==&h=NzcxNmU4YTJjNWMxM2EzNGQxMGIxZjhhZGFkMTVjMjJhODM5NjNlYjBlODhlYjk0ZGZjM2I2Zjc0ZmM3MWM1Yw==&p=YzJ1OnBsYW50YW5kZm9vZHJlc2VhcmNoOmM6bzoxYzczZGRhOWQ5NDRjOTQzZjU1YjkyNzg2YWViNTlkMjo3Omg6VA==>, or unsubscribe<https://checkpoint.url-protection.com/v1/r01/url?o=https%3A//github.com/notifications/unsubscribe-auth/ACECZT6XKXBOTVRNZPU4WFT2M22IPAVCNFSM6AAAAABV7FISWOVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYTIMRSGQZTGMI&g=MzkyNjRhMjQ4MjM2MGMwMw==&h=NTAxZTA4ZmEzZTU3Mjc3MDcyMjVjZDU5OGRmMzQwMTU1M2I1YzA1OWQ2YzgzNzE3YWQ1ZTc1YzcxYTFkODI0Zg==&p=YzJ1OnBsYW50YW5kZm9vZHJlc2VhcmNoOmM6bzoxYzczZGRhOWQ5NDRjOTQzZjU1YjkyNzg2YWViNTlkMjo3Omg6VA==>. You are receiving this because you were assigned.Message ID: ***@***.***> The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.