MAGeCK is pulling conditions instead of unique sample names

[jeremymsimon]

Description of the bug

I have an experimental setup with biological triplicates of my conditions: treated_5hr, treated_7hr, and control. My sample names as specified in the samplesheet look like

treated_5hr_1
treated_5hr_2
treated_5hr_3
treated_7hr_1
treated_7hr_2
treated_7hr_3
control_1
control_2
control_3

However my MAGeCK-count log shows my sample labels as

--sample-label treated_5hr,treated_5hr,treated_5hr,treated_7hr,treated_7hr,treated_7hr,control,control,control

As a result, I can't tell my replicates apart in my counts tables (count_table.count.txt , count_table.count_normalized.txt)

sgRNA   Gene    treated_5hr     treated_5hr     treated_5hr     treated_7hr     treated_7hr     treated_7hr     control control control
sgRNA1976       CD28    303     315     134     207     374     438     399     281     329
sgRNA56069      POTEB2  350     652     587     555     501     784     558     785     509
sgRNA37077      ZC2HC1C 224     53      43      121     0       57      308     73      76
sgRNA7735       KRT5    571     458     393     396     533     811     339     278     352
sgRNA9783       OPRM1   164     39      67      167     386     120     177     145     107
[...]

Is there an additional metadata column I can pass in my samplesheet, or is there another parameter somewhere I've missed? Or is this somehow pulling names from the condition column instead?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[nick-phillips]

+1, any suggested workaround for this?

[matbonfanti]

Hi @nick-phillips and @jeremymsimon,

I have recently been involved in the development of the pipeline, and I have experienced the same problem that you are describing. I think that there is no workaround, but I think that this can easily be fixed.

I will open a PR to try to change the sample labels in the mageck command line, and let you know!

[matbonfanti]

closed by #252