Hi all,
I have data from a single-end run with a dual index structure generated by the NextSeq 500 instrument. I want to do the demultiplexing by bcl2fastq
tool. How should my SampleSheet.csv
structure and bcl2fastq
script look like?
I used aSampleSheet
structure (shared below) with a bcl2fastq
command (mentioned below) and I got only 18% of reads undetermined
which I think is a good ratio (total number of reads was around 76 million and ~14 million reads were undetermined).
The SampleSheet.csv
structure. The index
column is for index i7 and the index2
column is for index i5.
[Header],,,
[Reads],,,
[Settings],,,
adapter,,,
,,,
[Data],,,
Sample_ID,Sample_Name,Description,index,index2
1_mESCs,1_mESCs,,AACCGCGG,CTAGCGCT
2_mESCs,2_mESCs,,GGTTATAA,CTAGCGCT
The bcl2fastq
script is as below.
bcl2fastq --runfolder-dir --output-dir --sample-sheet --barcode-mismatches 0
Is the overall approach correct? Should I include the --use-bases-mask
option as well?
Thank you for your input.
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