Creating annotation files

Question

[Shagnik]

Hi, I am trying this for the first time and need help. I have the genomic fasta file and annotation file (.gff3) for the draft genome of my (lesser known) model organism. I wish to grep and make a separate annotation file with only my selected regions (eg, genes related to Wnt signaling, genes related to Notch signaling, only ncRNA regions, etc). How do I fish out my specific regions into a separate GTF annotation file and use it for specific downstream processing? The scaffold IDs of my regions (relevant to the function) also need to be known. How do I gather those?

Answer 1

[Istvan Albert]

not clear what the question is, though, if you have a GFF file and the regions of interest are in there, then use the GFF file to generate the sequences then later select the sequences with the correct id. Is that what you are having problems with?

bedtools getfasta

or

gffread

programs can be used to extract sequences from genome using interval files

[Shagnik]

Thanks! It worked with gffread. Thanks