converting bcl file from MiSeq

[wingtec]

Hi All,

I wonder if anyone knows the trick of modifying the config.xml file generated in Illumina MiSeq runs so that a CASAVA or OLB can convert bcl files into fastq files. I understand that usually there is no need to do it since the secondary analysis in the MiSeq Reporter will do it automatically. But we did run into some errors which led to interruption of the secondary analysis so now we need to manually convert the bcl files into fastq files for further analysis.

Many thanks

Wingtec

[ECO]

We are awaiting the same answer from ILMN. Any run error (or canceling it early), means you have to manually do BCL-->FASTQ off the instrument. Baffles me that such simple things still elude a company that has been doing this for longer than anyone.

Will update if I hear.

[Sam64]

Hi,

You had an answer of Illumina ?

thank you to update if you had a solution

Sam

Paris, France

[GenoMax]

You can do the conversion of the BCL files off-line if you have access to CASAVA. We keep the analysis on our MiSeq turned off and handle the secondary data analysis off-line.