Hello everyone,

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
OK, so you want to annotate (predict genes) on a genomic sequence making use of RNAseq info. 

The question is easily asked but I'm afraid you might be underestimating how a complex matter this can be. But is absolute a good and correct approach. Problem is that this often requires quite a bit of work and knowledge. There are (or you could) run most tools as a black box but then your results will be of lesser quality. 

You might consider tools as: Maker, Braker, Augustus, ... (most of these use RNAseq as an evidence information but also require other inputs ). There will be others that might work with RNAseq only but none come to mind right now.
