Question: How do I process single cell data from non-recommended sequence run configurations?
Answer: If 10x Single Cell libraries are sequenced in a configuration that differs from our recommended sequencing configuration (Read 1: 26 cycles, i7 index: 8 cycles, Read 2: 98 cycles), it is possible to set the
--use-bases-mask option in
cellranger mkfastq to select only the cycles needed for downstream analysis. This will mask the extra bases from appearing in your FASTQ files, which will also save some disk space. For more information on the
cellranger mkfastq tool please see: Generating FASTQs.
Alternatively, if FASTQ files are generated using the Illumina
bcl2fastq software, the FASTQ files can be used directly in Cell Ranger. By default,
cellranger count will use only the first 26 bases from Read 1. Optionally the
--r1-length option can be set to trim the length of Read 1 to 26 bp and
--r2-length to trim Read 2 to a shorter length.
For more information on using FASTQ files directly from
bcl2fastq please see Using bcl2fastq directly.
For more information on the
cellranger count tool, see Single Library Analysis.