different results each the CITE-seq count is run

[colin986]

Hi,

I'm getting a different output each time CITE-seq count is run. My whitelist and parameters do not each each time.

Is this expected? Is there anyway to control this in terms of reproducibility (i.e. setting a seed) ?

Thanks, Colin

[Hoohm]

Hey Colin, This is really strange as there is no randomness in the code, it should pretty much be the exact same output each time for the same parameters.

Could you show me some examples?

On Fri, 11 Mar 2022, 22:05 colin986, @.***> wrote:

Hi,

I'm getting a different output each time CITE-seq count is run. My whitelist and parameters do not each each time.

Is this expected? Is there anyway to control this in terms of reproducibility (i.e. setting a seed) ?

Thanks, Colin

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[colin986]

Hi Hoohm,

Thanks for coming back to me.

You were right. The CITE-seq count output is the same each time.

The variation in the result seems to come from the HTODemux function in Seurat when using clara clustering option (When using kmeans clustering the output is consistent). The result changes each time I run CITE-Seq count. The function has an option to set the seed, but I've still found that the output changes each time. So what I mean here is that HTODemux is reproducible with the same CITE-seq count output. CITE-seq count is also reproducible. However, when I re-run CITE-Seq count and HTODemux I get a different result - I don't understand why this is happening.

I know HTODemux draws 100 samples from the dataset for clara clustering - I wonder if during the CITE-Seq count the samples, while the same, the data are written in a a different order and the 100 samples are drawn in a different order - and that gives rise to variability in the output?

Thanks, Colin