Annotate Single Cell Reads
Annotate Single Cell Reads can be found in the Toolbox here:
Toolbox | Single Cell Analysis (
) | Annotate Single Cell Reads (
)
The tool takes as input one or more Sequence Lists (
). For each input it outputs an 'annotated reads' sequence list, where reads only contain the biological sequence and are annotated with cell barcode, UMI and/or hashtag, as relevant. These reads can be used as input for:
- Single Cell RNA-Seq Analysis, see Single Cell RNA-Seq Analysis
- Map Reads to Reference, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Map_Reads_Reference.html, to produce a read mapping for Single Cell ATAC-Seq Analysis, see Single Cell ATAC-Seq Analysis
- Single Cell V(D)J-Seq Analysis, see Single Cell V(D)J-Seq Analysis
- Create Cell Annotations from Hashtags, see Create Cell Annotations from Hashtags
The cell barcode can be obtained as a combination of nucleotides from the read structure (see Read structure), part of the read name, and part of the input name (see Barcodes from names). The cell barcode needs to be defined through at least one of these three options.
Subsections
- Read structure
- Barcodes from names
- Barcode correction
- Sample name
- The output of Annotate Single Cell Reads