Redesign DEG folders - Githubissues

CCBR / Pipeliner

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

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Redesign DEG folders #324

Closed kopardev closed 5 years ago

kopardev commented 6 years ago

Need to add an extra column to "contrasts.tab", which will serve as an CPM cutoff threshold for the contrast represented on that line in the file.
all sample DEG folder separate (generated during initialQC)
DEG_RSEMgenes_ as folder name of each contrast. --filter each contrasts separtely --create separate PCA of contrast-only groups

skchronicles commented 5 years ago

Additions have been added to activeDev (two new columns are required for contrasts.txt) New format goes like: grp1 grp2 cpmThreshold minSampleThreshold

Example: KO WT 0.5 2 KO WT 0.5 1

Creates the following DE directories: DEG_KO-WT_0.5_2/ DEG_KO-WT_0.5_2/