Chromatin Accessibility Analysis from Reads
The workflow Chromatin Accessibility Analysis from Reads takes Reads as input and starts by annotating them with cell barcode and UMI, followed by trimming and mapping to create a Peak Count Matrix (
). Then it performs clustering. The workflow uses iterate functionality and allows for a combined analysis of multiple samples to produce:
- a single multi-sample Peak Count Matrix ();
- a Dimensionality Reduction Plot (
) associated with the automated clusters.
The workflow can be found in the Template Workflows section here:
Single Cell Workflows (
) | From Reads (
) | Chromatin Accessibility Analysis from Reads (
)
If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
You can choose either one or more Sequence lists or Select files for import and select FASTQ files for importing.
The workflow offers a number of options described below. Note that not all parameters can be configured. Open parameters indicate places where customization may be necessary for different samples, but default settings are suitable in most cases.
The workflow can be run using Single Cell hg38 (Ensembl) or Single Cell Mouse (Ensembl) reference data sets (see The Reference Data Manager).
|
Note: Reference data elements cannot be configured during workflow execution. If other elements than those provided in the default reference data sets are needed, a custom reference data set can be used, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Custom_Sets.html. |
The workflow allows the analysis of multiple samples and you can specify metadata during workflow execution for configuring which inputs belong to which sample. When there is only one library per sample, metadata is not necessary and "Use organization of input data" can be used. For more details on configuring workflow execution with metadata, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html. Make sure to inspect the batch overview to check that the analysis will be performed correctly.
Subsections
- Configuring the batch units for Chromatin Accessibility Analysis from Reads
- Output from Chromatin Accessibility Analysis from Reads