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 |
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
#!/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