Hello, I am demultiplexing some samples with bcl2fastq and I wonder if it is possible to avoid the addition of the barcode sequence to the header of the reads.
Many thanks, Goren
P.D: In the next steps I will use UMI-tools for adding the UMI sequence to the header, so I need to get rid of the barcode first.
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UMI-tools is perfectly happy with having the Illumina barcode in the normal spot, it adds UMIs to the read names.
Okey, I will try UMI-tools without removing the barcode and see if it works. Thanks!
It worked!! Thank you very much
Nope. No special options, no post processing. Version 2.19 if I remember right. Indices are included in the undetermined fastq file, but not the sample fastqs.
Actually, I see that it depends on the instrument. I run the same version and command line of bcl2fastq on the Miseq, and I see indices in the headers, but my Hiseq1000 fastq files do not have indices in the headers
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I don't think you can (if you are truly demultiplexing the data using
bcl2fastq). You will need to do it after the fact.