genomic-barcode-counter

A julia script that counts the number of barcodes (given as input) from fastq files.

Introduction

This respository consists of 3 scripts and 2 tools. I have also provided 2 shell scripts to run these tools.

barcodeCounter.jl A script that simply calls the fucntions in barcodeCountFuncts.jl to create an output file that contains the counts of each barcode identified in the barcode library provided to it.

barcodeCounterFuncts.jl Contains helper functions for barcodeCounter.

combineFiles.jl If the user is analyzing different runs, the user can use this script to combine all the *.counts files created by the barcodeCounter.jl script to form one singular count. The output is in a .tsv format made from a dataframe.

run.sh Runs barcodeCounter on one fastq file.

runAll.sh Runs barcodeCounter on all fastq files in the specified directory and runs combineFiles.jl to merge all files into one tsv file.

Requirements

julia v1.4.3

Julia Packages

• CSV v.0.8.4 (only used in combineFiles.jl)
• DataFrames v1.1.1 (only used in combineFiles.jl)
• DelimitedFiles
• FASTX v1.1.3
• Glob v.1.3.0 (onlyi used in combineFiles.jl)

Tools

barcodeCounter

Consists of the scripts barcodeCounter.jl and barcodeCounterFuncts.jl. To run this tool you will need to call the barcodeCounter.jl script.

The barcodeCounter.jl script has 3 arguments:

1. A fastq file
2. A barcode library formatted similar to promotor_library_barcodes.txt.
3. A file containing the spacer sequence (note: multiple spacer sequences are not supported yet, if you need it, start an issue and I'll try to get on that asap).

After the script runs successfully, the script outputs a .counts file in a tsv format that contains the following 3 rows:

1. barcode sequence
2. barcode name (as defined by the library)
3. barcode count (the number of times the barcode sequence appeard in the file passed in)

If you want to run the script without the provided run script, look at run.sh.

combineFiles

Combines all .count files into a singular TSV. combineFiles.jl will combine all the scripts inside of the directory of which it is called.

The TSV that is output has the following columns:

1. barcode sequence
2. barcode name
3. first file count results

    ...

    n. n'th file count results

Therefore, there will be a total of n+3 columns where n is the number of .count files in the directory.