Analyze#

Identify differentially abundant genes between the control (the inoculum) and treatment conditons with mbarq analyze#

Input/Output Files#

Required Inputs

  • Count file produced by mbarq merge

barcode

Name

Sample1

Sample2

…

ACCTGGTAG

geneA

500

1000

…

ACCGGGGAA

geneA

100

500

…

CCCGGGAAA

geneB

300

300

…

  • Sample data file (CSV) in the following format:

sampleID

batch

treatment

Sample1

B1

control

Sample2

B1

treatment1

…

…

…

  • Name of the column indicating batch in the sample data should be specified using --batch_column (For the example above, --batch_column batch)

  • Name of the column indicating treatment in the sample data should be specified using --treatment_column (for the example above, --treatment_column treatment)

  • Treatment level that should be used as a control/baseline should be specified using --baseline (for the example above, --baseline control)

Suggested Inputs

  • We highly recommend adding control strains (i.e. strains with barcodes inserted into fitness-neutral locations) to the barcode library. This greatly facilitates quality control and analysis of the data.

  • If control strains are present in the library, the control barcodes can be specified with control file using --control_file option.

    • In the simplest option, control file will only contain the barcode sequences of the control strains (1 barcode per line).

    • If different control strains were added at different concentrations, the concentration of each barcode can be specified in the second column.

    • If control strains included strains of different genotypes (ex. wild type as well as negative control strains), the genotype can be specified in the 3rd column.

    • Only wild type strains will be used for quality control and analysis. This should be specified as wt, WT, or wildtype.

    • The control file should be in CSV format, and contain NO header.

[Required]

[Optional]

[Optional]

ACCTGGGTT

0.005

wt

CCGGAAGGT

0.001

wt

Output Files

Example Usage#

mbarq analyze -i <count_file> -s <sample_data_file> -c <control_file> \ 
--treatment_column treatment --batch_column batch --baseline control

All Options#

mbarq analyze
Usage: mbarq analyze <options>

Options:
  -i, --count_file FILE    CSV file produced by `mbarq merge`
  -s, --sample_data FILE   CSV file containing sample data
  -c, --control_file FILE  control barcode file, see documentation for proper
                           format
  -g, --gene_name STR      column in the count file containing gene
                           identifiers [Name]
  --treatment_column STR   column in sample data file indicating treatment
  --batch_column STR       column in sample data file indicating batch
  --baseline STR           treatment level to use as control/baseline, ex.
                           day0
  -n, --name STR           experiment name, by default will try to use count
                           file name
  -o, --out_dir DIR        Output directory
  -h, --help               Show this message and exit.