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Hoohm avatar Hoohm commented on July 26, 2024

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naila53 avatar naila53 commented on July 26, 2024

Hi,
I set the cells parameter to 1million, just thinking of retrieving empty droplets. That's too high right?

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Hoohm avatar Hoohm commented on July 26, 2024

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naila53 avatar naila53 commented on July 26, 2024

hi, I need to retrieve the empty droplets for the sake of normalization, to model noise component. I have run your method about a year ago and you can see I posted a different issue here about totalseqB #158
but the point is I used high number of cells as you can see in my run info to retrieve the empty droplets.
I tried again with inputting the raw unfiltered cellranger barcodes list as a whitelist for my data
and kept the -cells argument at 1million cells , it still keeps getting stuck at the final step for hours! and it looks like it's trying to process more than 1million!
I think something has changed in the new version, because it ran fine on all my previous totalseqA data..
image

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Hoohm avatar Hoohm commented on July 26, 2024

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naila53 avatar naila53 commented on July 26, 2024

thank you so much for your prompt response! I tried reinstalling the older version( 1.4.3) and I seem to have resolved this. However, I tried to reproduce my previous analysis, I seem to have a new issue with both new and old version where it fails at the very last step!
any ideas? :(
image

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Hoohm avatar Hoohm commented on July 26, 2024

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naila53 avatar naila53 commented on July 26, 2024

yes, it is! installed python 3.7 and worked! thank you so much!

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