Does Illumina's bcl2fastq command line tool have a way to pipe to stdout immediately
Does Illumina's bcl2fastq command line utility have a way to pipe the base calls immediately to stdout? Right now I have to wait the 1 hour or so it takes for bcl2fastq to make a gzip file that I can unzip. I'd like to immediately pipe this data to stdout if possible. I don't see a command line option in the documentation to do this. If this is not possible; is there any application that will immediately pipe these calls to stdout?
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b10hazard •
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I don't think so. If you just want no compression on the files then run
bcl2fastqwith the following option.You would still not be able to use the files until the run is done.