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While processing 10x Chromium Single Cell Multiome ATAC + Gene Expression sequencing data via ‘cellranger-arc count’ pipeline, Feature linkages analysis is performed as pairs of genomic features, such as peaks and genes, that have significant correlation in signals across cells. Because it provides a basis for inferring enhancer-gene targeting relationships and constructing transcriptional networks. The features with strong linkages are considered to be “co-expressed” and enriched for a shared regulatory mechanism.
Partek Flow provides the opportunity to our users to explore the linkage relationships among different features including peaks and genes, peaks and peaks, and genes and genes. A tab-delimited file containing information of feature linkages inferred from Flow Cell Ranger - ATAC task will be loaded into Integrative Genome Viewer (IGV) for exploration if Feature linkage analysis task has been completed successfully.
Running Feature linkage analysis
To run Feature linkage analysis task (Figure 1),
Figure 1. Feature linkage analysis task in Flow
There will be no inputs needed if the FASTQ is converted to counts matrix within Flow. However, if users processed the FASTQ files outside of Partek, and imported the counts matrix into Flow later. The feature_linkage.bedpe file in outs/analysis/feature_linkage from Cell Ranger output will be needed for each sample (Figure 2) to complete the analysis.
A new datanode will be displayed as the task is finished. Double click on the output datanode, Flow will bring you to the IGV browser where you could explore the “co-expressed”feature pairs (Figure 3).
The feature_linkage.bedpe file outputted from Cell Ranger pipeline is available in task report as a table. In the report table, each row is a region of a peak and includes the following information:
To filter out and visualize only the linkages that users are interested in is also made possible through the Filter feature linkages task in Flow (Figure 4). Users are able to download the .bedpe file from Flow and explore them via their stand-alone IGV.
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