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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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ATAC- Cell Ranger ARC #193

Closed jiangzh-coder closed 8 months ago

jiangzh-coder commented 1 year ago

Hi，

If i analyzed10xgenomics ATAC- Cell Ranger ARC dataset，can i do following?

  1. For ATAC- Cell Ranger ARC-count， can i use sra datasets（scRNAseq+scATACseq), transformed them into FASTQ files by using fasterq-dump or parallel-fastq-dump, then rename them? https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc https://www.jianshu.com/p/36dc29ae0ed9 https://kb.10xgenomics.com/hc/en-us/articles/360061165691-Can-I-analyze-only-the-ATAC-data-from-my-single-cell-multiome-experiment-

  2. For ATAC- Cell Ranger ARC-count， how can i index reference genome？ https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references https://support.10xgenomics.com/single-cell-atac/software/release-notes/references https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/tutorial/mkref

thanks and best wishes Jiang

evolvedmicrobe commented 1 year ago

Hi, please reach out to support@10xgenomics.com who will be able to help you with this.