How to use transcript coverage for ORF calls on contig?
I have a metagenomics assembly and I've identified several contigs that are bona fide viral contigs (I used virsorter2 and checkv). I have paired metatranscriptomics data for these samples and I mapped to the viral contigs. I then converted those bam files to bed files using bedtools genomecov.
Is there any way I can use the coverage profiles with the contig assembly to get better ORF calls than prodigal?
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