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Tip revision: 44f72a1e27db1bafefb159cdc26bc71f3691bf54 authored by Behzad Yaghmaeian Salmani on 07 March 2024, 16:41:19 UTC
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Tip revision: 44f72a1

# Get Mouse reference (mm10) dataset required for Cell Ranger.
# Download - 9.6 GB - md5sum: 8ce6bc561e2554701fc43871301042e6

curl -O
# or 

# make a Cell Ranger compatible "pre-mRNA" reference package according to the instructions:


### bash script for cellranger count 


module add bioinfo-tools
module add cellranger/3.0.1

# Define variables

# Get list of sample names from their paths
SAMPLES=($(ls -d "$FASTQ_DIR"/* | awk -F'/' '{print $NF}'))

# Loop through sample names
for SAMPLE_ID in "${SAMPLES[@]}"; do
    echo "Processing sample: $SAMPLE_ID"
    # Run cellranger count command
    cellranger count \
        --id="$SAMPLE_ID" \
        --fastqs="$FASTQ_DIR/$SAMPLE_ID" \
    echo "Sample $SAMPLE_ID processing complete."

echo "All samples processed."

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