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Ivarz / Conifer

Calculate confidence scores from Kraken2 output
BSD 2-Clause "Simplified" License
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conifer output not to specific readIDs #7

Closed ellyyuyang closed 2 years ago

ellyyuyang commented 2 years ago

Hello,

Thanks for developing this tool! I have recently come across it and thought it would help me to fine tune the accuracy of my Kraken2 results. I read in the readme file that it generates the confidence scores for each readID. However, in my conifer output file, I see the confidence score for each taxid/taxname, as opposed to readID. Is there anything I did wrong?

Thanks, Elly

Ivarz commented 2 years ago

Dear Elly,

Sorry for delayed response. Conifer assigns confidence scores for each read by default. However, if you are using flag -s, then score summary per taxonomy will be reported instead. So you should probably remove -s flag from the command.

Hope this helps, Ivars

ellyyuyang commented 2 years ago

Dear Ivars,

I see, got it! Thanks for your reply!

Best, Elly