mkfastqsupports a new sequencing configuration for Novaseq where the I2 index may need to be reverse-complemented before demultiplexing dual-indexed libraries. countandvdjrunapproximately two to four times fasterthan in Cell Ranger 3.1, depending on the sequencing data, and reduces disk I/O by hal...
cellranger mkfastq will select the appropriate mode depending on the sample indexes used, and enable index-hopping filtering automatically for dual-indexed flow cells. For example, with the Dual Index Kit TT Set A, well A1 can be specified in the sample sheet as "SI-TT-A1", and cell...
Where Read Type is one of: I1: Dual index i7 read (optional) I2: Dual index i5 read (optional) R1: Read 1 R2: Read 2 链接:https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/fastq-input#gex_rightname 如果fq的文件名格式不对,在运行的过程中会...
cellranger-atac工作流程的第一步是从BCL(BCL 文件是原始的测序文件,来自 Illumina 测序仪)文件格式转换为FASTQ文件格式,这是通过cellranger-atac mkfastq工具完成的。cellranger-atac mkfastq是基于 Illumina 的bcl2fastq工具的一个封装,并增加了许多...
If used, navigate to the specified directory first and then run mkfastq. --samplesheet Optional. Path to an Illumina Experiment Manager-compatible sample sheet which contains 10x Genomics sample index names (e.g., SI-GA-A1 or SI-TT-A12) in the sample index column. All other information, ...
dual-indexed flow cells. For example, with the Dual Index Kit TT Set A, well A1 can be specified in the sample sheet as "SI-TT-A1", andcellranger mkfastqwill recognize the i7 and i5 indices asGTAACATGCGandAGTGTTACCT, respectively. Similarly for Single Index Kit T Set A, well A1 ...
cellranger mkfastq will select the appropriate mode depending on the sample indexes used, and enable index-hopping filtering automatically for dual-indexed flow cells. For example, with the Dual Index Kit TT Set A, well A1 can be specified in the sample sheet as "SI-TT-A1", and cell...
I2: Dual index i5 read (optional) R1: Read 1 R2: Read 2 链接:https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/fastq-input#gex_rightname 如果fq的文件名格式不对,在运行的过程中会出现错误,所以最开始需要确定文件名的格式以及进行修改。习惯是重新创建一...
Thecellranger-dna mkfastqpipeline can also be run with a samplesheet in the Illumina Experiment Manager (IEM) format. If you didn't sequence with an i7 index, you'll need to use this format. Let's briefly look atcellranger-dna-tiny-bcl-samplesheet-1.0.0.csvbefore running the pipeline....
mkfastq Usage: Copy cellranger mkfastq --help cellranger mkfastq --run=PATH [options] ArgumentDescription --runRequired. The path of Illumina BCL run folder. --idOptional. Defaults to the name of the flow cell referred to by--run. Name of the folder created bymkfastq. This option does...