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parmejohn / scRNA-pipeline-UofM

scRNA-seq Pipeline for Drogemoller and Wright Labs
GNU General Public License v3.0
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add an option to increase # of genes considered for slingshot DEG list #26

Closed parmejohn closed 4 months ago

parmejohn commented 4 months ago

Right now the default is 100 genes for the sake of compilation time, but this is probably missing biological importance. Going to run it without size limit on GReX and monitoring the time and memory used.

parmejohn commented 4 months ago

Runtime when including all genes for small dataset for trajectory DEG does not seem bad. Keep all for full run and compare runtimes.

parmejohn commented 4 months ago

Out of memory error occurred with over 450 GB memory in GReX. Possibly due to new processes occurring simultaneously. Need to fix so that only differentially expressed ones are printed

parmejohn commented 4 months ago

Default to select the top 100 genes with new associationTest implementation

parmejohn commented 4 months ago

take only the top 50 genes to make trajectory DEG more legible