fasta_data.sh

fastq_data.sh - Basic analysis of raw fastq file data

Usage:

fastq_data.sh <fastq_file>

Where <fastq_file> is a fastq file to be analyzed

This script takes a fastq file as input and produces a pdf file containing a brief summary of the data and accompanying plots which can be used to assess sequence quality. This is achieved using the seqTools package in R.

Input fastq file must have .fq or .fastq extension.

Output will be named:

fastq_data_results-<fastq_file>.pdf  

Example:

fastq_data.sh read1.fastq  

Output:

fastq_data_results-read1.fastq.pdf  

This script requires that seqTools library be available in your R installation.