sra to gzipped fastq

One way to take NCBI's SRA format to a gzipped fastq file (since BWA can take a gzipped fastq as input) is to pipe the SRA Toolkit's fastq-dump to gzip and direct that to an output file. Here's an example that uses the -X flag to only take 10 spots from the SRA file to test it out:
#Get an sra file:

#Designate where the SRAToolkit executables are

#fastq-dump converts the sra format to fastq format. -X designates how many spots to convert, and -Z designates to write to stdout.
${SRATOOLKITBIN}fastq-dump -X 10 -Z SRR771638.sra | gzip > SRR771638.fasta.gz

echo "Finished compression"

#Take a peek at the gzipped file.
gunzip -c SRR771638.fasta.gz | head -n 10


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