kopardev
commented
6 years ago - PCA part of initial QC
- DEG_ALL folder is created during initialQC for all sample reporting
- All subread (gene/gene_junction/junction) output is reported to DEG_ALL
- All sample RSEM output is reported to DEG_ALL
- extra column in contrasts.tab for cpm cutoff
- create "DEG< group1 >-< group2 >< cpm_cutoff >" folders in the working folder
- contrasts specific RSEM output (only groups in contrast) is reported in "DEG< group1 >-< group2 >< cpm_cutoff >" ... it is preformated to integer from float.
- DEG only performed for RSEM_genes for now
- groups.tab is required to run initial qc ... this is not reflected in the GUI
- same contrasts can be rerun with different cpm_cutoffs
- old "DEG_*" folders are removed