Dear All I need to make a gff/gtf annotation file to map RNA-seq data. Reference genome is available as a multiple fasta files at NCBI. I have downloaded these files (approx. 300) and compiled to use it for reference genome. NCBI has already annotated genes present in every BAC separately. But I don't know how to import these sequences with annotation. For example, http://www.ncbi.nlm.nih.gov/nuccore/KF184657.1 is a BAC fasta file, by clicking the protein in the right-side-pane it shows the genes present in this FASTA. How to import these listed genes in an annotation file. Another way to do this task could be, first map reads on simply BACs sequences without any annotation file(if that's possible) and the after getting transcripts, identify them with Batch homology searches for genes OR some other analysis. Please help if you have any clue to how to solve this problem step-wise. THANKYOU.
