Confirming that separate conditions/treatments should be analyzed by separate pipelines

[OrangeyO2]

Hello

Apologies if this question is redundant, but I just wanted to make sure I was correct.

Following up on these previous questions,

67 #225 #258

separate conditions/treatments should have separate input json files, and be analyzed separately, am I correct?

Therefore, an input json file should only contain fastqs from the same condition/treatment, differing only in biological/technical replicates, and if there are 3 treatments (e.g. drug A, drug B, untreated), I should run the pipeline 3 times.

Thanks in advance for your help!

[akundaje]

Yes correct

On Mon, Nov 27, 2023, 10:23 PM OrangeyO2 @.***> wrote:

Hello

Apologies if this question is redundant, but I just wanted to make sure I was correct.

Following up on these previous questions,

67 https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/67 #225

https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/225 #258 https://github.com/ENCODE-DCC/atac-seq-pipeline/issues/258

separate conditions/treatments should have separate input json files, and be analyzed separately, am I correct?

Therefore, an input json file should only contain fastqs from the same condition/treatment, differing only in biological/technical replicates, and if there are 3 treatments (e.g. drug A, drug B, untreated), I should run the pipeline 3 times.

Thanks in advance for your help!

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[OrangeyO2]

Thank you!