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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
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DTR #44

Closed SergeyBaikal closed 1 year ago

SergeyBaikal commented 1 year ago

Dear, Mike I found that not all contigs with DTR are added to the final file (final_combined_virus_sequences). Why can this be? For example, 4 contigs with DTR were found, but only 1 in the final file. I can send a file with contigs.

SergeyBaikal commented 1 year ago

I probably understood. Because the first step is checking with the content of the DTR, and the second is the search for the HMM profile, probably at the first step the sequences found with the DTR are not viral. Is it so? My contigs from metagenomic data.

mtisza1 commented 1 year ago

Sergey, it looks like you've figured out the logic. As you say, Cenote-Taker 2 first catalogs all the sequences with DTRs (these could be plasmids or replicative intermediates of non-viral mobile genetic elements, for example), but only DTR contigs with hallmark genes are kept for the final report.

If you want to get genome maps for all DTR contigs, you can use --circ_minimum_hallmark_genes 0.

SergeyBaikal commented 1 year ago

Thanks a lot for your answer, Mike!