Single Cell ATAC-Seq Analysis

Single Cell ATAC-Seq Analysis can be found in the Toolbox here:

        Toolbox | Single Cell Analysis (Image sc_folder_closed_16_n_p) | Chromatin Accessibility (Image sc_atac_seq_folder_open_16_n_p) | Single Cell ATAC-Seq Analysis (Image sc_atac_seq_peak_16_n_p)

The tool takes as input a single read mapping (Image read_track_16_n_p) of reads that have been annotated using Annotate Single Cell Reads. The tool outputs:

It is important that the input read mapping contains all the samples that will be used in a downstream analysis. This is because it is not possible to combine Peak Count Matrices as they will typically have different coordinates for shared peaks. There are two ways to generate a single read mapping from multiple samples:

  1. Provide multiple read lists to Map Reads to Reference https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Map_Reads_Reference.html.
  2. Merge existing read mappings using Merge Read Mappings https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Merge_Read_Mappings.html.

The tool requires a Peak Shape Filter (Image graph) for calling scATAC-Seq peaks, and both a Gene track (Image annotation_track_16_n_p) and a corresponding mRNA track (Image annotation_track_16_n_p) for assigning nearby genes to peaks. These data can be directly downloaded using the Reference Data Manager (see Reference data management).

It is also possible to supply custom Peak Shape Filter, Gene track and mRNA track as follows:

The following additional options are available:



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