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Feature: Automatically determine sample type using gene expression #30

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mdshw5 opened this issue Sep 16, 2022 · 0 comments

Open

5 tasks

Feature: Automatically determine sample type using gene expression #30

mdshw5 opened this issue Sep 16, 2022 · 0 comments

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mdshw5 commented Sep 16, 2022 •

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add "housekeeping genes" parameter to config.json
add code to build "housekeeping" salmon index files for determining sample type
add code to sequentially load these index files and quantify the first 1e6 reads
add code to sum counts for "housekeeping" quant.sf files and determine most likely sample type composition
add argument parser to expose new auto sample type determination

mdshw5 self-assigned this

mdshw5 added the enhancement label

mdshw5 changed the title ~~Automatically determine sample type~~ Feature: Automatically determine sample type using gene expression

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