Hi everyone, I've made an assembly for a chloroplast genome, however I'm confused as to what I have to do next...
I'm trying to identify any genes that are normally present in chloroplasts but are missing in my assembly. How could I go about doing this?
I've already identified my plant based on phylogenies focusing on rbcL genes and rps4+rps4-trnS intergenic spacer. I have the fasta of the assembly and I've seen people using bedtools but I don't know which commands to use (if I use bowtie2 to make a .sam output, wouldn't that just use my non-assembled sequences? since I used getorganelle to assemble my genome and all I have from that is the fasta.
Thank you so much.