README.md

sci-L3-target-seq primer designer

Introduction

Prerequisites

python=3.6
pandas=1.0.1
biopython
bedtools=2.29.1
primer3 (libprimer3 release 2.5.0)

or create and activate environment.yaml in the "scripts" directory

    $ conda env create -f ./scripts/environment.yaml  
    $ conda activate sci-L3-target-seq-primers

Usage

Prepare input files

1. Create a BED6 file containing the regions to be targetted.

    Tab-delimited 6 columns with .bed extension:
    [chromosome, region start, region end, unique gene/exon name (without spaces), score(default 1 for all), strand(+ or -)]
    Example:
        chr9	133589332	133589842	ABL1_Ex1	1	+
        chr9	133729450	133729624	ABL1_Ex2	1	+

2. Create a CSV file containing a list of barcodes for the universal primers

3. Create a CSV file containing a list of sample specific indices

Run

$ python ./scripts/run.py -i <path to bed file> -g <path to fasta file of reference genome> -b <path to .CSV file of barcodes> -indices <path to .CSV file with sample specific indices> [options]

Optional Arguments

-h, --help                  show this help message and exit
-i, --input                 Enter the path to the BED or FASTA file
-g, --genome                Enter the path to the reference genome
--P5, -P5                   P5 Adapter sequence(Default=AATGATACGGCGACCACCGAGA)
--P7, -P7                   P7 Adapter sequence(Default=CAAGCAGAAGACGGCATACGAGAT)
--read1, -r1                Read1 sequence(Default=TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG)
--read2, -r2                Read2 sequence(Default=GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG)
--SSSPR, -ssspr             SSS Primer Region(Default=GGGATGCAGCTCGCTCCTG)
--indices, -indices         Enter the path to the CSV file containing sample specific indices
--barcodes, -b              Enter the path to the CSV file containing Barcodes