Gene annotation file and assembly difference?

Question

[nishag]

I'd like to use ASpli package to determine alternative splicing event in my transcriptome data. For that, I need to have the gene annotation file for my species. However, I'm very confused with the term gene annotation file and assembly file. Assemblies are found in bam format and annotation files are found in gff format. I'm very confused as the RefSEq assembly that I have downloded is in gff format. How to confirm gene annotation files?

Answer 1

[lieven.sterck]

Assembly files are usually in fasta format (.fa / .tfa / .fasta or such) and they contain the actual genome/transcript sequences (== stretches of A C G T ).

Annotation files usually come indeed in GFF, EMBL, GB formats and contain the location of genic and other features on the sequences as you have them from the assembly files . These are plain txt files (tab delineated eg for GFF files).

EMBL & GenBank (GB) format can sometimes be a combined version: they then contain both the actual sequence as the corresponding (gene) annotation on them