Bartender
Bartender is a c++ tool that is designed to process random barcode data. Bartender is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
It currently has three functionalities.
It extracts barcodes from FASTA or FASTQ files.
It clusters barcode reads and counts the frequency of each cluster.
It generates count trajectories for time-course data.
Version | module name |
|---|---|
1.1 | bartender/1.1 |
Example: /share/Apps/examples/bartender
#!/bin/bash
#SBATCH -p lts
#SBATCH -t 60
#SBATCH -n 1
#SBATCH -N 5
module load bartender
cd /share/Apps/examples/bartender
bartender_single_com -f random_small_data/2M_extracted_barcode.txt -o 2M_barcode -d 3
bartender_single_com -f random_small_data/2M_extracted_barcode_umi.txt -o 2M_barcodei_umi -d 3
bartender_extractor_com -f random_small_data/2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2 -d both
bartender_extractor_com -f random_small_data/2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2 --direction=forward -u 0,10
echo "Deleting Files created"
rm -rf 2Mbarcode*
cd simulation_data
echo "This example requires 26GB RAM"
tar -xvzf simulated_data.tar.gz
bash clustering_test.sh
echo "Deleting Files created"
rm -rf cluster_result_new_barcode.csv cluster_result_new_cluster.csv cluster_result_new_quality.csv simulation_data.csv
For more information visit https://github.com/LaoZZZZZ/bartender-1.1
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