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bhattlab / phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
MIT License
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Question of reads mapped #32

Closed wen1112 closed 1 year ago

wen1112 commented 1 year ago

Hi, I would like to know how to obtain the mapping information for each individual read when I perform sample analysis using Phanta. Similar to how I can determine the mapping status of each read and which genome it is mapped to in the SAM file.

meenachakra commented 1 year ago

Hi, you can specify False for delete_intermediate in the config and use the .krak files in the classification/intermediate folder.

wen1112 commented 1 year ago

Thank you! I will try it.