Hi, we were running a 1x126bp high-output run on our HiSeq, but a comms issue caused the run to fail at cycle 109. Basecalling was complete however for cycles 1-107, although for some reason Q30% drops to about 50% after cycle 99. However, since the user only needs ~100bp of data, I would like to process the basecalls as they stand.
What would I need to do in order for bcl2fastq to correctly process the data assuming I treat it as a 1x101bp run? Modify the runinfo/runparameters.xml files to alter read length and set usebasesmask to y101nnnnn (or something like that)? Or would I also need to copy the various RTAcomplete and BasecallingComplete.txt files from a successful run?
Thanks,
Matt
What would I need to do in order for bcl2fastq to correctly process the data assuming I treat it as a 1x101bp run? Modify the runinfo/runparameters.xml files to alter read length and set usebasesmask to y101nnnnn (or something like that)? Or would I also need to copy the various RTAcomplete and BasecallingComplete.txt files from a successful run?
Thanks,
Matt
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