How to annotate chloroplast genome with a .gff file of the entire organism?

Question

[tmrhyd]

Hey all,

I know some of my past posts haven't made too much sense, so I hope this makes sense.

I have a .gff file with the annotations for the entire genome of my plant species, and I want to use it to annotate just the chloroplast genome. How do I extract or apply just that part of the .gff file to my chloroplast files(formatted as a VCF and .bam files). Is it possible to use IGV and my .gff file to annotate my VCF and bam files? (of my organisms genome mapped against the chloroplast genome).

Thank you so much in advance!!

[GenoMax]

Is it possible to use IGV and my .gff file to annotate my VCF and bam files?

Yes/No. If you are looking to view your BAM/VCF files to see how the alignments/SNPs look against the reference then yes. But no if you want to permanently annotate your VCF files. IGV, as the name indicates, is mainly a genome viewer.

As for extraction of annotations from gff file, if you know the identifier used in your GTF file for the chloroplast genome you could use grep id_for_chloro_genome your.gff > chloro.gff to extract the relevant lines.

I want to use it to annotate just the chloroplast genome.

What do you exactly mean when you say that? You already have the annotations (presumably) in your GFF file.

[tmrhyd]

I aligned my chloroplast reference Fasta against the genome of a modified version of my original plant, and now have the VCF of that vs the original plant genome aligned against the same chloroplast reference fasta. I have the .gff that has all the annotations for the entire original plant genome and am using IGV to look at the variants between the two Bam files (original vs modified, both aligned against the chloroplast reference) and I need the annotations so I can identify the variants I am looking at in IGV.

So as far as I can tell, I need the annotations in the .gff file to display in IGV for just the chloroplast.

I hope this explains it, I'm sorry if some of the terminology Is wrong!!

[GenoMax]

First let us clarify terminology you are using/referring to. You are working with just chloroplast genome(s) and relevant chloroplast reference. Is that correct?

What is original and modified referring to?

aligned my chloroplast reference Fasta against the genome of a modified version of my original plant,

I assume you mean your own chloroplast assembly against reference chloroplast genome or did you align against the whole genome?

I have the .gff that has all the annotations for the entire original plant genome

If plastid/chloroplast genome is indeed separate than your original genome then .gff will have no annotations about chloroplast genome in it.

Are you aware of the Organelle genome resource at NCBI that has sequences for chloroplast genomes available?