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Feature: Automatically determine sample type using gene expression

Open mdshw5 opened this issue 3 years ago • 0 comments

  • [ ] 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

h/t @singerj

mdshw5 avatar Sep 16 '22 15:09 mdshw5