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Fastq files

Links for this experiment

Study information at the Sequence Read Archive:

http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP033351

Himes et al paper at PubMed Central:

http://www.ncbi.nlm.nih.gov/pubmed/24926665

Example sample table stored in our course repo on github:

https://github.com/genomicsclass/labs/blob/master/course5/airway_sample_table.csv

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

http://www.bioconductor.org/packages/release/data/experiment/vignettes/airway/inst/doc/airway.html

The European Nucleotide Archive (EMBL-EBI):

http://www.ebi.ac.uk/ena

The Sequence Read Archive (NCBI):

http://www.ncbi.nlm.nih.gov/sra/

Fastq file commands

Downloading from the ENA:

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz

Alias for ls:

alias ll='ls -lGh'

Unzipping:

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