#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dump is in the SRA toolkit. It allows directly downloading data from a particular sequencing run ID
fastq-dump --split-files SRR1770413
#SRA stores data in a particular compressed format (SRA!) that isn't directly compatible with any downstream tools, so it's necessary to put things into FASTQ for further processing. The --split-files part of the command ensures we get two files, one for the first and second mate in each pair. We'll use them in this format when aligning.
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR1770413/SRR1770413.sra
sra-dump --split-files SRR1770413.sra
