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Old 05-12-2017, 03:53 AM   #9
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Location: Germany

Join Date: Apr 2012
Posts: 215

Originally Posted by GenoMax View Post
Some of us do not use the on-board analysis software for MiSeq, so we transfer (in fact save in real time) the entire raw data folder to a network share for off-line analysis with bcl2fastq. With some longer/well loaded runs this data can be close to 30+G.
And what is the advantage of doing so? I thought "GenerateFastq" is the smallest, possible workflow I can use for a run? In that workflow fastqs are generated by applying bcl2fastq internally after the run has been completed. At least that is what the technician told us when the machine was installed (at least my ~2 year old notes tell me so ).
I also compared once self-made bcl2fastq output to the existing fastqs in the output folder and there was no difference. Currently, I would only perform a conversion myself if the used indices are diverse and a lot of reads were classified as "undetermined" to "rescue" some of them (but this never happened so far).
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