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wososa / PSI-Sigma

PSI-Sigma
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Is the .bam file in the groupa.txt and groupb.txt files, fixed in relation to the control group, experimental group? #69

Closed happypiggyzjx closed 4 weeks ago

happypiggyzjx commented 2 months ago

Hi Woody,

For the groupa.txt file and groupb.txt file in the command, must it be the .bam file for the control group in a and the .bam file for the experimental group in b? (I see an example of this in PPT1 on your github)

When I ran the command, I thought that the two groups were just difference groups, in no order, and I was given the name of the bam file for the experimental group in groupa, and the name of the bam file for the control group in groupb. Does this affect my output?

Best, happypiggy

happypiggyzjx commented 2 months ago

PS: I tried switching the order for experimentation and didn't notice a difference, but wanted to consult you for insurance purposes~

wososa commented 1 month ago

Hi @happypiggyzjx ,

Sorry for the late reply. I missed your messages. Switching from groupa to groupb should only influences the delta-PSI values. You can define anything as “Control” (or ‘groupa’). Hope that this answers your question.

Best, Woody

wososa commented 4 weeks ago

@happypiggyzjx ,

I assume that you have found your solution, so I am closing the issue now.

Best, Woody