VisiumTrim

TSO and polyA trimming of fastq files generated with 10x Visium

Installation

Clone repository:

git clone https://github.com/ludvigla/VisiumTrim

Install cutadapt:

pip install cutadapt

Make sure that the script is executable:

chmod +x TSO_polyA_trimming.sh

Usage

Instructions:

./TSO_polyA_trimming.sh --help

Trim a fastq file with default settings:

./TSO_polyA_trimming.sh R2_fastq.gz

Adjust minimal polyA homopolymer length (default 10):

./TSO_polyA_trimming.sh R2_fastq.gz -l 15

Adjust error tolerance for adapter search (default 0.1):

./TSO_polyA_trimming.sh R2_fastq.gz -e 0

Adjust overlap (minimal length of partial match, default 5):

./TSO_polyA_trimming.sh R2_fastq.gz --overlap 10

Change output path:

./TSO_polyA_trimming.sh R2_fastq.gz -o trimmed_R2.fastq.gz