Bartender

Usage

Bartender

usage: Bartender [-h] [--output_dir] [--run_name] [--experimental_file] [--stock_file] [--upstream_nucleotide_match]
                 [--downstream_nucleotide_match] [--barcode_length] [--hamming_distance] [--no_copy] [--dry]

options:
  -h, --help            show this help message and exit
  --output_dir
                        Path to output directory
  --run_name RUN_NAME   Name of the run
  --experimental_file
                        Path to experimental input csv file [None]
  --stock_file
                        Path to stock input csv file [None]
  --upstream_nucleotide_match
                        Upstream nucleotide sequence to match [TAGCATAA]
  --downstream_nucleotide_match
                        Downstream nucleotide sequence to match [ATGGAAGAA]
  --barcode_length
                        Length of barcode to capture [35]
  --hamming_distance
                        Hamming distance to find closest potential barcode [3]
  --no_copy             Don't make a copy of the work folder prior to a run [False]
  --dry                 Print arguments and exit program [False]

Bartender reports

usage: BartenderReport [-h] [--run_dir] [--experimental_report] [--stock_report] [--report_table_type_1] [--experimental_trend_width] [--experimental_trend_height]
                   [--per_experimental_group_width] [--per_experimental_group_height] [--dry] [--Rscript_path]

options:
  -h, --help            show this help message and exit
  --run_dir             Path to run directory [None]
  --experimental_summary_table
                        Make experimental summary table [False]
  --experimental_report
                        Make experimental report [False]
  --stock_report        Make stock report [False]
  --report_table_type_1
                        Make report table with counts [False]
  --experimental_trend_width
                        Width [15]
  --experimental_trend_height
                        Height [15]
  --per_experimental_group_width
                        Width [15]
  --per_experimental_group_height
                        Height [15]
  --dry                 Print arguments and exit program [False]
  --Rscript_path RSCRIPT_PATH
                        Path to Rscript [/usr/bin/]

Example input tables

Stock

sample_name	biological_group	input_template	R1	R2
stock_1	CD4_derived_TF	50000	/path/to/stock_1_S1_L001_R1_001.trimmed.fastq.gz	/path/to/stock_1_S1_L001_R2_001.trimmed.fastq.gz
stock_2	CD4_derived_TF	50000	/path/to/stock_2_S2_L001_R1_001.trimmed.fastq.gz	/path/to/stock_2_S2_L001_R2_001.trimmed.fastq.gz
stock_3	CD4_derived_TF	50000	/path/to/stock_3_S3_L001_R1_001.trimmed.fastq.gz	/path/to/stock_3_S3_L001_R2_001.trimmed.fastq.gz
stock_4	CD4_derived_TF	50000	/path/to/stock_4_S4_L001_R1_001.trimmed.fastq.gz	/path/to/stock_4_S4_L001_R2_001.trimmed.fastq.gz
stock_5	CD4_derived_TF	50000	/path/to/stock_5_S5_L001_R1_001.trimmed.fastq.gz	/path/to/stock_5_S5_L001_R2_001.trimmed.fastq.gz

Experimental

sample_name	biological_group	cell_type	time_point	time_point_description	organ	input_template	genetic_source	R1	R2
sample1_d27_PLASMA_S12	animal1	unknown	27	unknown	plasma	10000	dna	/path/to/sample1_d27_PLASMA_S12_L001_R1_001.trimmed.fastq.gz	/path/to/sample1_d27_PLASMA_S12_L001_R2_001.trimmed.fastq.gz
sample2_d27_PLASMA_S20	animal1	unknown	27	unknown	plasma	10000	dna	/path/to/sample2_d27_PLASMA_S20_L001_R1_001.trimmed.fastq.gz	/path/to/sample2_d27_PLASMA_S20_L001_R2_001.trimmed.fastq.gz
sample3_d27_PLASMA_S21	animal2	unknown	27	unknown	plasma	10000	dna	/path/to/sample3_d27_PLASMA_S21_L001_R1_001.trimmed.fastq.gz	/path/to/sample3_d27_PLASMA_S21_L001_R2_001.trimmed.fastq.gz
sample4_d27_PLASMA_S22	animal1	unknown	27	unknown	plasma	10000	dna	/path/to/sample4_d27_PLASMA_S22_L001_R1_001.trimmed.fastq.gz	/path/to/sample4_d27_PLASMA_S22_L001_R2_001.trimmed.fastq.gz
sample5_d27_PLASMA_S22	animal3	unknown	27	unknown	plasma	10000	dna	/path/to/sample5_d27_PLASMA_S5_L001_R1_001.trimmed.fastq.gz	/path/to/sample5_d27_PLASMA_S5_L001_R2_001.trimmed.fastq.gz