I have recently binned a whole lot of contigs, coming from a metagenomic sample. I have merged all my bins into one file, but the fasta-headers (>bin-name) have descriptions about what bacterial taxonomy the contig represents.
The next step was to annotate the genes of my bins. When i annotate the genes (with Prokka/Prodigal), I get a single file, with all predicted genes. However, I have no way of knowing what gene belongs to what bacteria, since the bacterial taxonomy headers are not preserved.
Do you guys have any ideas on how to know what genes belong to what bacteria? I would rather not run the bins 1 by 1, as I have thousands of them, and it would generate thousands of files to manage (that's why i merged all the bins).