cellranger code

Author: craniolab

.gitignore

@@ -4,3 +4,4 @@ figures_ignore/
 cellranger_related/cellranger_output/
 cellranger_related/cellranger-9.0.1/
 cellranger_related/cellranger-atac-2.1.0/
+sequencing_results/

cellranger_related/cellranger_code/cellranger_count/run_catshark.sh

@@ -0,0 +1,44 @@
+#!/bin/sh 
+#SBATCH --job-name=cellranger 
+#SBATCH --partition=standard
+#SBATCH --nodes=1 
+#SBATCH --time=4-0 
+#SBATCH --mem=250G 
+#SBATCH --ntasks=16 
+#SBATCH --error=job.%J.err 
+#SBATCH --out=job.%J.out 
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=SE10 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/catshark/sScyCan1.1/SE10 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/sScyCan1_1 \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/catshark \
+																						  --sample=SE10 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=SE8_9 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/catshark/sScyCan1.1/SE8_9 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/sScyCan1_1 \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/catshark \
+																						  --sample=SE8_9 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																						  
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=SE11 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/catshark/sScyCan1.1/SE11 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/sScyCan1_1 \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/catshark \
+																						  --sample=SE11 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																						  
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=SE12 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/catshark/sScyCan1.1/SE12 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/sScyCan1_1 \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/catshark \
+																						  --sample=SE12 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248

cellranger_related/cellranger_code/cellranger_count/run_chicken.sh

@@ -0,0 +1,53 @@
+#!/bin/sh 
+#SBATCH --job-name=cellranger 
+#SBATCH --partition=standard
+#SBATCH --nodes=1 
+#SBATCH --time=4-0 
+#SBATCH --mem=250G 
+#SBATCH --ntasks=16 
+#SBATCH --error=job.%J.err 
+#SBATCH --out=job.%J.out 
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD1 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg6a/CkD1 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg6a \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD1 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD2 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg6a/CkD2 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg6a \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD2 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																					
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD3 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg6a/CkD3 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg6a \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD3 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																						  
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD4 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg6a/CkD4 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg6a \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD4 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD5 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg6a/CkD5 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg6a \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD5 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248																						  

cellranger_related/cellranger_code/cellranger_count/run_chicken_2.sh

@@ -0,0 +1,53 @@
+#!/bin/sh 
+#SBATCH --job-name=cellranger 
+#SBATCH --partition=standard
+#SBATCH --nodes=1 
+#SBATCH --time=4-0 
+#SBATCH --mem=250G 
+#SBATCH --ntasks=16 
+#SBATCH --error=job.%J.err 
+#SBATCH --out=job.%J.out 
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD1 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg7b/CkD1 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg7b \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD1 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD2 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg7b/CkD2 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg7b \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD2 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD3 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg7b/CkD3 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg7b \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD3 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																						  
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD4 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg7b/CkD4 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg7b \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD4 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248
+																						  
+/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/cellranger count --id=CkD5 \
+																						  --output-dir=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger_output/sc_rnaseq/chicken/GRCg7b/CkD5 \
+																						  --transcriptome=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/cellranger_related/cellranger-9.0.1/reference_genomes/GRCg7b \
+																						  --fastqs=/groups/mpistaff/Cranio_Lab/Louk_Seton/4_species_project/sequencing_results/sc_rnaseq/chicken \
+																						  --sample=CkD5 \
+																						  --create-bam=true \
+																						  --localcores=16 \
+																						  --localmem=248