fastq.gz and fastq

[Masta]

Is their a way to compare those two using 'bwa' etc.?!?
I need to compare a set of fastq files with the 1000gp project data

[dawe]

bwa supports plain text and gzipped fastq as well (as most of the software available), so you only have to run your alignments. You will compare results according to what you are interested to.
Alternatively you can compare your fastq files from a QC point of view, using FastQC or similar tools.

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