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Fastq files

Links for this experiment

Study information at the Sequence Read Archive:

Himes et al paper at PubMed Central:

Example sample table stored in our course repo on github:

Details on creating such a sample table from SRA and GEO:

The European Nucleotide Archive (EMBL-EBI):

The Sequence Read Archive (NCBI):

Fastq file commands

Downloading from the ENA:


Alias for ls:

alias ll='ls -lGh'


gunzip *.fastq.gz

Looking at the FASTQ files:

less SRR1039508_1.fastq
wc -l SRR1039508_1.fastq

Quality control with fastqc

fastqc --noextract SRR1039508_1.fastq SRR1039508_2.fastq