Per Illumina, we use n+1 cycles for n-bp read lengths (e.g. 2x151 cycles for 2x150bp reads). Out of curiosity, how do other sequencing providers typically handle that last +1 base? Do you:
1) include the +1 base in your FASTQ output and let clients deal with it?
2) trim after demultiplexing (e.g. using Trimmomatic)?
3) mask during demultiplexing (e.g. using --use-bases-mask)
4) other...?
A bit of background, we use both MiSeq and Nextseq instruments, and have resorted to manually running bcl2fastq.
1) include the +1 base in your FASTQ output and let clients deal with it?
2) trim after demultiplexing (e.g. using Trimmomatic)?
3) mask during demultiplexing (e.g. using --use-bases-mask)
4) other...?
A bit of background, we use both MiSeq and Nextseq instruments, and have resorted to manually running bcl2fastq.
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