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 |
#!/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
