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

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