I am really new in this forum, so I hope you can help me in resolving my problem. I am actually working on a project, where I have to annotate some sequences.these sequences are a result of rna_seq , and I have them in bam format. Do you know some easy bioinformatics tools that can help me to annnotate that kind of sequences in order to get GFF files ?? So the input should be in bam files and the output in GFF. Just for information, i need a tool that can be executed in linux, and that can be looped for so many sequences for different species.
Thank you for your help