Keeping your FASTQ read files in gzip compressed format saves much of the precious space of you hard drives. Unfortunately, there are still some tools that do not support direct use of compressed files. For many tools, the following trick will work.
gunzip -c mate1.fastq.gz > mate1.fastq &
gunzip -c mate2.fastq.gz > mate2.fastq &
bowtie -S genome -1 mate1.fastq -2 mate2.fastq > sample.sam
ecSeq is a bioinformatics solution provider with solid expertise in the analysis of high-throughput sequencing data. We can help you to get the most out of your sequencing experiments by developing data analysis strategies and expert consulting. We organize public workshops and conduct on-site trainings on NGS data analysis.
Last updated on May 06, 2013