countTags - counting a set of k-mers into a set of FASTQ files

Installation

1. Clone this repository : git clone https://github.com/jaudoux/countTags.git
2. Compile the software : make
3. Place the binary somewhere acessible in your $PATH

Usage

First you need to create a FASTA file containing the tags you want to quantify. All tags must have the same length, and the maximum authorize lenght is 32bp. K-mer length must be provided to countTags using the -k INT option.

For example :

countTags -k 31 file.fa file1.fastq.gz file2.fastq.gz

Managing Paired-End files

For paired-end files, you need to apply a post treatment to merge counts produced separatly for each fastq file.

Managing stranded files

For stranded fastq, you need to set the --stranded option. If you are using PE stranded FASTQ files, you need to manually reverse one of the pair according to the protocol orientation.