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Combine gene annotations (from metagenomes) & gene coverage information into single file

I was wondering if anyone had recommendations for how to merge gene annotation & coverage results into a single file? I have outputs from KoFamScan with specific KO IDs & functions per gene ID (attached image of text file), and outputs from MosDepth which contains coverage per gene ID in my contigs (attached image of BED file).

I would love to somehow create a file that combines all of these data into a single file, showing gene ID, assigned function or KO ID, & coverage/thresholds of coverage.

Unfortunately, there are tons of repeated geneIDs in the KoFamScan output as well as the MosDepth output files, and I am a bit stuck… I would like to only merge the top 5 best hits per gene ID from KoFamScan, but that’s less urgent at the moment.

Any advice or suggestions for how to do this are greatly appreciated, than you so much! enter image description here

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coverage kofamscan metagenome annotation functional mosdepth
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written by lintonf • lintonf

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