Illumina NextSeq SampleSheets

Question

[pablominguez]

Hi all,

I have a illumina run with several projects inside (TruSeq Amplicon and Nextera Rapid Capture) and I cannot find how to configure the SampleSheet.csv to include for example the Assay type which are different or the adpaters. I just want to run bcl2fastq and at the moment I am creating separated SampleSheets and the run bcl2fastq with each one but really not sure if this will work. Does anyone know if I can just edit a single SampleSheet.csv and how :) .. or I have to work with several ones?

Thanks a lot!

[pablominguez]

Perfect, both solutions seems to work. Thanks a lot!

Answer 1

[GenoMax]

If you are demultiplexing the data off-instrument there is no problem using multiple samplesheets and corresponding bcl2fastq v.2 runs.

Answer 2

[Devon Ryan]

Assuming things like adapter type/length don't vary within a lane, then you can use the masking features of bcl2fastq rather than making multiple sample sheets.