Chris:LabNotes/General Protocols/BaseCalling Procedure
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Illumina Demultiplexing Procedure
- Below is a procedure to take the raw basecall data from an Illumina run and output fastq files for all specified indices
Download Data from Basespace
- We want to download the run folder from Basespace. This can either be done by physically copying the files onto a flash drive from the sequencer or downloaded online following instructions from Dinh's labwiki <http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-3-25>
Basecalling using bcl2fastq
- Once we have the raw data, we next want to demultiplex