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CCBR / CRISPIN

CRISPR screen pipeline
https://ccbr.github.io/CRISPIN/
MIT License
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automatically pull col names to be analyzed with BAGEL #33

Open slsevilla opened 11 months ago

slsevilla commented 11 months ago

Description of the bug

Currently pipeline requires the user to input the columns to be analyzed within BAGEL.

According to documentation the -c flag in BAGEL is for the -c [columns to test]. Numbering begins after the GENE column with 1 through N cols. The columns to be tested are dependent on the samplesheet input and will be inconsistent and difficult for the user to identify.

For FC -c flag is control columns (check to see how to handle more than one column)

For BF -c flag is treatment columns at the same time

REFERENCE: https://htmlpreview.github.io/?https://github.com/hart-lab/bagel/blob/master/BAGEL-v2-tutorial.html

Proposed Solution

Will need to change the -c flag from controls col to treatment cols depending on the input