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CCBR / CRISPIN

CRISPR screen pipeline
https://ccbr.github.io/CRISPIN/
MIT License
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MAGeCK fails when counts matrix has an empty geneID #34

Open slsevilla opened 11 months ago

slsevilla commented 11 months ago

Description of the bug

During mageck test pipeline is failing

 mageck test \
    -k cruise_1.count.txt \
    -t D8_KO_Dabrafenib_R1,D8_KO_Dabrafenib_R2,D8_KO_Dabrafenib_R3,D8_KO_Dabrafenib_R4 \
    -c D8_KO_DMSO_R1,D8_KO_DMSO_R2,D8_KO_DMSO_R3,D8_KO_DMSO_R4 \
    -n cruise_1
ERROR @ Mon, 20 Nov 2023 00:04:45: Error: empty gene ID is not allowed at line 268. Please double-check your read count table file.

When reviewing the contrast table cruise_1.count.txt this line has no geneID.

Proposed solution

Add in a check for the library that each row has three columns