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clb21565 / kairos

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Confusion about the output #6

Open Wang0293 opened 3 months ago

Wang0293 commented 3 months ago

Hi, @clb21565

I have two problems about the derep-detect output.

1) How are potential HGT events counted using the potential HGT results? For example, is each line of the output result in phylum_HGT.csv represent an HGT event, even if all the mobile_target_gene, mge_hgt, and target_hgt are 0, 0, 0?

2) What is the first column in the phylum_HGT.csv?

HGT

clb21565 commented 3 months ago

Hello there, and thank you for your interest in kairos! Re. 1, Yes it is likely the majority of detected HGTs will not involve target genes and or mges. The target/mge columns generally point to the most interesting potential HGTs depending on the research question, but I do count ones without the hits when considering the overall number of potential HGT events.

The first column is just the index produced during python data wrangling and is just a unique identifier for the row, and not really meaningful here.

I also noted your emails and will respond to your other questions as soon as I can.

Wang0293 commented 3 months ago

I know that, very thanks for your time.