这3个样品,每个样品都有4个合格的文件名字,就可以跑cellranger-atac 的 流程啦,代码也很简单: $ cat run-cellranger_hg38.sh bin=/pipeline/cellranger-atac-2.1.0/bin/cellranger-atac db=/pipeline/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 ls$bin; ls$db fq_dir=/jmzeng/2022-PRJNA768891-ccRCC...
这3个样品,每个样品都有4个合格的文件名字,就可以跑cellranger-atac 的 流程啦,代码也很简单 $ cat run-cellranger_hg38.sh bin=/pipeline/cellranger-atac-2.1.0/bin/cellranger-atac db=/pipeline/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 ls $bin; ls $db fq_dir=/jmzeng/2022-PRJNA768891-ccR...
/ceshi/spatial/spaceranger_tutorial/spaceranger-2.1.1/spaceranger count \ #首先要写软件在的绝对路径,但是如果这个路径已经被写入./bashac文件的话,那就不需要写软件的绝对路径了 --id=Colon \ #输出的文件夹名字 --transcriptome=/fastq/genome/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \ #参考基因...
Runcellranger-arc mkfastqon the Illumina BCL output folder for each ATAC (GEX resp.) flow cell to generate ATAC (GEX resp.) FASTQ data. Note that a separate run ofmkfastqis required for each ATAC and each GEX flow cell. Run a separate instance ofcellranger-arc countfor eachGEM welltha...
单细胞多组学ATAC- Cell Ranger ARC--count 单细胞多组学ATAC-Cellranger ARC-结果解读之网页报告【有一个系列】 多样本合并: gene很好合并,但是peak不行,必须合在一起call peak才行,所以必须在上游就处理完成; Aggregating Multiple GEM Wells with cellranger-arc aggr ...
Cell Ranger ATAC and ARC software have just received some major improvements! Update to Cell Ranger ATAC v2 and Cell Ranger ARC v2 to see how these powerful tools for computational analysis of single cell open chromatin and transcriptional data have gotten even better....
Cell Ranger ATAC and ARC software have just received some major improvements! Update to Cell Ranger ATAC v2 and Cell Ranger ARC v2 to see how these powerful tools for computational analysis of single cell open chromatin and transcriptional data have gotten even better....
Cell Ranger ARC analyzes data generated by the Chromium Single Cell Multiome ATAC + Gene Expression assay to compute sequencing quality and application result metrics for each supported library type. Supported library types are "Gene Expression" and "Chromatin Accessibility". The pipeline outputs key...
1 condainstall-c dranew bcl2fastq 参考: Generating FASTQs with cellranger-arc mkfastq Running cellranger mkfastq
528M 3月 24 10:50 cellranger-atac-2.1.0.tar.gz 14G 5月 3 2021 refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz 因为必须去ncbi的sra下载,大家可以参考前面的系列教程。 这个项目就3个10x的单细胞ATAC数据,但是文件实在是有点大,所以耗时一天半,sra文件如下所示: ...