scRNAbox with processed data
Contents
- Introduction
- From Step 2: Create Seurat object and remove ambient RNA
- From Step 3: Quality control and filtering
- From Step 4: Demultiplexing and doublet removal
- From Step 5: Integration and linear dimensional reduction
- From Step 6: Clustering
- From Step 7: Cluster annotation
- From Step 8: Differential gene expression contrasts
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