Update README_SCRNA.md

README_SCRNA.md

@@ -147,29 +147,32 @@ bash $SCRNABOX_HOME/launch_scrnabox.sh \
 --enrich T
 ```
 
-Otherwise, run the enrichment directly:
+Otherwise, run the enrichment directly in R:
 ```
+dir.create("$SCRNABOX_PWD/step7/annot")
 level_cluster='integrated_snn_res.0.7'
-ClusterMarkers='/SCRNABOX_PWD/step7/info7/ClusterMarkers.rds'
-PWD='/SCRNABOX_PWD/step7/annot/'
-PSUE='/SCRNABOX_PWD/step6/objs/seu_step6.rds'
+ClusterMarkers='$SCRNABOX_PWD/step7/info7/ClusterMarkers.rds'
+PWD='$SCRNABOX_PWD/step7/annot/'
+PSUE='$SCRNABOX_PWD/step6/objs6/seu_step6.rds'
 top_sel=5
 db <- c('Descartes_Cell_Types_and_Tissue_2021','CellMarker_Augmented_2021','Azimuth_Cell_Types_2021')
 scrnaboxR::annotation(level_cluster,ClusterMarkers,PWD,PSUE,top_sel,db)
 ```
 
 To run enrichment on your PC, first copy it to your PC, 
 ```
-scp -r [email protected]:${SCRNABOX_PWD}/step7 ~/Desktop/annot/
-scp -r [email protected]:${SCRNABOX_PWD}/step6 ~/Desktop/annot/
+mkdir ~/Desktop/des/
+scp -r [email protected]:${SCRNABOX_PWD}/step7 ~/Desktop/des/
+scp -r [email protected]:${SCRNABOX_PWD}/step6 ~/Desktop/des/
+mkdir ~/Desktop/des/step7/annot
 ```
 
 Then run the following codes
 ```
 level_cluster='integrated_snn_res.0.7'
 ClusterMarkers='~/Desktop/annot/step7/info7/ClusterMarkers.rds'
-PWD='~/Desktop/annot/'
-PSUE='~/Desktop/annot/step6/objs/seu_step6.rds'
+PWD='~/Desktop/des/step7/annot/'
+PSUE='~/Desktop/des/step6/objs/seu_step6.rds'
 top_sel=5
 db <- c('Descartes_Cell_Types_and_Tissue_2021','CellMarker_Augmented_2021','Azimuth_Cell_Types_2021')
 scrnaboxR::annotation(level_cluster,PWD,PSUE,top_sel,db)