REcount Barcode Analysis
Code for analyzing REcount barcode sequencing data. The REcount_barcode_analysis.py program takes in a FASTQ file and barcode reference FASTA file and outputs a plot and a .txt file with barcode counts.
Prerequisites
Python 2.7
BioPython
Usage
REcount_barcode_analysis.py [-h] [-i] [-r] [-o] [-m]
optional arguments:
-h, --help show this help message and exit
-i , --input_file Input path for raw FASTQ file [required].
-r , --reference_file Input reference FASTA file [required].
-o , --output_dir Output directory for plot and barcode count file (default: same folder as input file)
-m , --mismatches_allowed Number of mismatches to barcode reference sequences allowed (default 2)
Usage example
REcount_barcode_analysis.py -i <PathToFile/InputFileName> -r <PathToFile/ReferenceFileName>