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statOmics / satuRn

satuRn is a highly performant and scalable method for performing differential transcript usage analyses.
https://statomics.github.io/satuRn/
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Preprocessing killed #30

Closed TdzBAS closed 1 year ago

TdzBAS commented 1 year ago

Hi Jeroen,

thanks for your wonderful tool! I havent faced any issues up until now. It is not directly connect to your tool, rather than to the preprocessing part before. Currently I create the countmatrix through the TPM columns from the quant.sf files which I get after quasi mapping with salmon. Attached is my script. But now I am working with a big dataset, with several 100 of cells and the merging process gets always killed. Do you have an efficient way to create the count matrix? I have access to an sungrid cluster, but even submitting to the cluster kills my job. Do you maybe have an efficient way/script which you can provide? Thanks!

My current script: sal_merge_fancy.txt

Best, Tolga

TdzBAS commented 1 year ago

could solve it by concatenating the dataframes :)

jgilis commented 1 year ago

Hi @TdzBAS,

Do you mean your issue is resolved now and I can close it?

Jeroen

TdzBAS commented 1 year ago

Hi @jgilis ,

yes, sorry for the circumstances. Best Tolga

jgilis commented 1 year ago

No worries at all, I am happy you found a solution. I will close the issue!