Question: What bcl2fastq
parameters does mkfastq
use internally? (Can I use other bcl2fastq
parameters, such as --ignore-missing-bcls
)?
Answer: Because mkfastq is just a thin wrapper around bcl2fastq, in addition to the commands documented in cellranger mkfastq --help
you can optionally pass other arguments through. These are the default parameters that cellranger mkfastq
passes to bcl2fastq
:
--minimum-trimmed-read-length 8
--mask-short-adapter-reads 8
--create-fastq-for-index-reads
--ignore-missing-positions
--ignore-missing-filter
--ignore-missing-bcls
--use-bases-mask=Y26,I8,Y98
-p 6 -d 6 -r 6 -w 6
mkfastq
does this during the BCL2FASTQ_WITH_SAMPLESHEET
stage:
For more information please consult Illumina's bcl2fastq documentation.