After running Evolinc 1.7.5 and Evolinc-Merge on the Discovery Environment, the output annotations have chromosome IDs of newly identified lincRNAs that do not match the parent (input) annotation.
The input annotation uses the nomenclature: 'Chr1', 'Chr2', 'Chr3', etc. and 'Scaffold12345'. The 'Final_updated.gtf' from Evolinc-Merge keeps this pattern for existing features, but new lincRNAs will lose the "Chr" identifier or the "Scaffold" identifier in column 1. Additionally, scaffold numbers that begin with a 0 in the parent annotation (e.g. "Scaffold00123") will lose those 0 values and will show "123" as the new chromosome.
Is this an issue for lincRNA identification if Evolinc is not able to assign the lincRNAs to the "known" chromosomes?
I have attached gzipped input and output annotations for your reference .
After running Evolinc 1.7.5 and Evolinc-Merge on the Discovery Environment, the output annotations have chromosome IDs of newly identified lincRNAs that do not match the parent (input) annotation.
The input annotation uses the nomenclature: 'Chr1', 'Chr2', 'Chr3', etc. and 'Scaffold12345'. The 'Final_updated.gtf' from Evolinc-Merge keeps this pattern for existing features, but new lincRNAs will lose the "Chr" identifier or the "Scaffold" identifier in column 1. Additionally, scaffold numbers that begin with a 0 in the parent annotation (e.g. "Scaffold00123") will lose those 0 values and will show "123" as the new chromosome.
Is this an issue for lincRNA identification if Evolinc is not able to assign the lincRNAs to the "known" chromosomes?
I have attached gzipped input and output annotations for your reference .
Thank you for your support. Final_updated.gtf.gz Cs_genes_v2.1_annot.gff3.gz