I have been trying to recover a crashed Illumina HiSeq 2500 run, but seemingly hit a wall.
The run was interrupted after a series of catastrophic events (power failure, generator failure, no-break failure). The run was interrupted, luckily, during index 2 sequencing, which is important to just one lane. Read 1 cif files were processed (and deleted afterwards) into bcl files by Illumina's RTA software, and I was able to get read 1 fastqs easily enough - after editing a corrupted config.xml file and using bcl2fastq.
However, read 2 cif files were not processed, so I have the cif files from cycles C141 to C250. I am trying to find out how to convert these cif to bcl, to no avail. It seems bustard needs all cif files to process them.
Any suggestions?
Sounds like a question for Illumina's tech support.
Hello h.mon!
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Sounds like a question for Illumina's tech support.
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:'(No problem, it is indeed a question much better suited to Illumina's tech support - I am waiting for their answer, in fact. I will try my luck at Seqanswers as well, it has a wider scope than Biostars.
I had reopened it because it is a bioinformatics problem.