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What is STARsolo?

STARsolo is a versatile tool developed for single-cell RNA sequencing analysis. It inputs the raw FASTQ reads files, and performs mapping, demultiplexing and quantification for single cell RNA-seq data. It follows CellRanger logic for cell barcode whitelisting and UMI deduplication, and produces nearly identical gene counts in the same format. STARsolo is also running much faster than the CellRanger[1].

Run STARsolo in Partek Flow

Partek® Flow® wraps STARsolo v2.7.11a and focuses on assays from 10X Genomics.

To run the STARsolo task for scATAC-Seq data, select the Unaligned reads data node, then select STARsolo in the 10x Genomics section (Figure 1). 

Once the task has been picked, a first time user will be asked to create a index file (Figure 2). Clicking the big blue button of Create star2.7.8a index would pop up a new window where lists the requirements that users need to fill in (right panel, Figure 2). 

Once the right options have been chosen, simply press the Create button to finish. The index of ‘ hg38 - Ensembl 99’ has been created as an example here (Figure 3).

The main task menu will be refreshed as above (Figure 3) for STARsolo task if index has been added. Users can go ahead select the Assay type before they click the Finish button to run the task. The STARsolo for this version only handles gene expression data no matter where it’s sourced from.

A new data node named Single cell counts will be displayed in Flow if the task has been completed successfully (Figure 4). Downstream analysis such as QA/QC, normalization, dimension reduction, clustering, differential analysis,  etc will start from the data node.

References

1. doi:https://doi.org/10.1101/2021.05.05.442755

Additional Assistance

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