scRNAbox with processed data

Contents


Introduction

This guide demonstrates how to initiate the scRNAbox pipeline at different Analytical Steps using processed data. The procedures are the same for both the Standard and Cell Hashtag Analysis Tracks.


From Step 2: Create Seurat object and remove ambient RNA

I have to return to this.


From Step 3: Quality control and filtering

If you have a Seurat object(s) and want to initiate the pipeline at Step 3, create a /step3/objs3 folder in the working directory, copy the Seurat object(s) to this folder, and run Step 3.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step3
cd step3
mkdir objs3
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step3/objs3

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 3

From Step 4: Demultiplexing and doublet removal

If you have a Seurat object(s) and want to initiate the pipeline at Step 4, create a /step4/objs4 folder in the working directory, copy the Seurat object(s) to this folder, and run Step 4.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step4
cd step4
mkdir objs4
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step4/objs4

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 4

From Step 5: Integration and linear dimensional reduction

If you have a Seurat object(s) and want to initiate the pipeline at Step 5, create a /step5/objs5 folder in the working directory, copy the Seurat object(s) to this folder, and run Step 5.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step5
cd step5
mkdir objs5
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step5/objs5

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 5

From Step 6: Clustering

If you have a Seurat object and want to initiate the pipeline at Step 6, create a /step6/objs6 folder in the working directory, copy the Seurat object to this folder, and run Step 6.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step6
cd step6
mkdir objs6
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step6/objs6

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 6

From Step 7: Cluster annotation

If you have a Seurat object and want to initiate the pipeline at Step 7, create a /step7/objs7 folder in the working directory, copy the Seurat object to this folder, and run Step 7.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step7
cd step7
mkdir objs7
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step7/objs7

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 7

From Step 8: Differential gene expression contrasts

If you have a Seurat object and want to initiate the pipeline at Step 8, create a /step8/objs8 folder in the working directory, copy the Seurat object to this folder, and run Step 8.

export SCRNABOX_PWD=/path/to/working/directory
cd ${SCRNABOX_PWD}
mkdir step8
cd step8
mkdir objs8
cp /path/to/Seurat/object ${SCRNABOX_PWD}/step8/objs8

bash $SCRNABOX_HOME/launch_scrnabox.sh \
-d ${SCRNABOX_PWD} \
--steps 8