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bjbvoesenek / qPCR-analysis

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Q: Should house keeping genes be configurable? #2

Closed ifokkema closed 1 year ago

ifokkema commented 1 year ago

Q: Should housekeeping genes be configurable?

I'm not 100% sure anymore, but I think I remember that you mentioned that the housekeeping genes should be configurable. If so, this code should be adapted to take these genes as arguments at runtime or from the input file through some method. https://github.com/bjbvoesenek/qPCR-analysis/blob/2b49bf13fba765547933ca3be6fe03b8499e2478/qpcr_analysis.py#L7-L9

If I remember wrong, feel free to close this issue.

bjbvoesenek commented 1 year ago

Yes, housekeeping genes differ per qPCR experiment and are chosen by the user! So indeed, the housekeeping genes should be provided in a similar (or the same) way as the 'number of PCR cycles' is provided in the 'Transpose' script.

bjbvoesenek commented 1 year ago

I didn't know exactly how this should look like in my code, that's why I left it like this. I will change it tomorrow

ifokkema commented 1 year ago

OK, cool! The most common method is to use command-line arguments for this; this allows both local users and the web wrapper to provide the information needed.

ifokkema commented 1 year ago

Fixed with 1bc0fdef1c01ff132cd71d0a63c702ad747ea122.