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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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Correcting for batch effects while running JUM #39

Open avantika-insitro opened 2 years ago

avantika-insitro commented 2 years ago

Running JUM v2.02, the example design file given in the manual contains only the experimental condition:

      condition
ctrl1 control
ctrl2 control
ctrl3 control
treat1 treatment
treat2 treatment
treat3 treatment

Is it possible to include batch effects (e.g. sequencing batch) in the experimental design for JUM? Would this be as simple as adding another column to the design matrix or more complex?

Thank you for the help!

qqwang-berkeley commented 1 year ago

I apologize for the late reply.

You can not just add another column to the design matrix to include batch effect. If you want to analyze the influence of batch effect on splicing, you need to, say, just take your control samples, and separate them into batch 1 and batch 2, and run JUM on these samples but change condition to "batch 1" and "batch 2".

On Wed, Jul 13, 2022 at 12:38 PM Avantika Lal @.***> wrote:

Running JUM v2.02, the example design file given in the manual contains only the experimental condition:

  condition

ctrl1 control ctrl2 control ctrl3 control treat1 treatment treat2 treatment treat3 treatment

Is it possible to include batch effects (e.g. sequencing batch) in the experimental design for JUM? Would this be as simple as adding another column to the design matrix or more complex?

Thank you for the help!

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