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Update pre-process-w-cellranger.md for CellRanger 9.0 #31

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Update pre-process-w-cellranger.md for CellRanger 9.0 #31

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15 changes: 8 additions & 7 deletions pre-process-w-cellranger.md
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Expand Up @@ -18,7 +18,7 @@ Here are the steps that need to be completed prior to running cellranger.

#### I have mouse or human

We have prebuilt references for mouse and human located here:
There are prebuilt references for mouse and human located on O2. For the paths, run `module spider cellranger`.

#### I have another genome

Expand All @@ -37,7 +37,7 @@ Below is an example script for a non-model reference
#SBATCH -c 1
#SBATCH --mem=48G

module load cellranger/7.1.0
module load cellranger/9.1.0

cellranger mkref \
--genome=my_nonmodel_genome \
Expand Down Expand Up @@ -117,8 +117,8 @@ Here is an example sbatch script for running cellranger as an array
```(bash)
#!/bin/bash

#SBATCH --job-name=CellRangerCount3 # Job name
#SBATCH --partition=short # Partition name
#SBATCH --job-name=CellRangerCount # Job name
#SBATCH --partition=short # Partition name
#SBATCH --time=0-05:00 # Runtime in D-HH:MM format
#SBATCH --nodes=1 # Number of nodes (keep at 1)
#SBATCH --ntasks=1 # Number of tasks per node (keep at 1)
Expand All @@ -128,14 +128,15 @@ Here is an example sbatch script for running cellranger as an array
#SBATCH --output=jobid_%j.out # File to which STDOUT will be written, including job ID


samp=$(awk -v awkvar="${SLURM_ARRAY_TASK_ID}" 'NR==awkvar' samples.txt) ### This line will take the numeric slurm array task id and find the corresponding line number in samples.txt. The sample name is made into a variable called samp.
samp=$(awk -v awkvar="${SLURM_ARRAY_TASK_ID}" 'NR==awkvar' samples.txt) ### This line will take the numeric slurm array task id and find the corresponding line number in samples.txt. The sample name is made into a variable called samp. This is also what your output folders will be called.

module load cellranger/7.1.0
module load cellranger/9.1.0

cellranger count \
--id=${samp} \ ## This is what your output folders will be named
--id=${samp} \
--fastqs=/path/to/your/folder/of/fastq/folders/${samp} \
--transcriptome=/path/to/your/genome \
--create-bam=false \
--localcores=16 \
--localmem=128

Expand Down