February 2022
The 10x library contains four pieces of information, in the form of DNA sequences, for each “read”.
The sequences for any given fragment will generally be delivered in 3 or 4 files:
The first steps in the analysis of single cell RNAseq data:
Alternative methods include:
Cell Ranger includes a number of different tools for analysing scRNAseq data, including:
cellranger mkref
- for making custom referencescellranger count
- for aligning reads and generating a count matrixcellranger aggr
- for combining multiple samples and normalising the countsCell Ranger requires the fastq file names to follow a convention:
<SampleName>_S<SampleNumber>_L00<Lane>_<Read>_001.fastq.gz
e.g. for a single sample in the Caron data set we have:
SRR9264343_S0_L001_I1_001.fastq.gz SRR9264343_S0_L001_R1_001.fastq.gz SRR9264343_S0_L001_R2_001.fastq.gz
As with other aligners Cell Ranger requires the information about the genome and transcriptome of interest to be provided in a specific format.
cellranger mkref
cellranger count