Hi all, I am working on galaxy and have a genome file in genbank format. To use featurecounts for my RNAseq, I need to convert the genbank format to a GTF format because that’s the format the featurecounts tool in galaxy expects. Now, I tried to convert thse genbank to GFF3 using GenbaktoGFF3 tool in galaxy and managed to do so. Also I tried to use the gffread tool to convert the GFF3 file to GTF but this resulted in a GTF with no written lines and I can’t understand why.
Is there a way to directly convert genbank to GTF in galaxy (or even outside galaxy, but preferably in galaxy). Also, any idea why gffread is not working properly in my case? I am using default parameters (leaving everything as is) and only giving GTF as feature file output and track name as “word”.