Running the CellTag workflow with just V1 dataset

morris-lab / BiddyetalWorkflow

This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.

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Running the CellTag workflow with just V1 dataset #5

Closed DnyanadaPande closed 2 years ago

DnyanadaPande commented 2 years ago

Hello,

I have a single-cell RNAseq dataset run with the CellTag-V1 library. I am running the Workflow and am able to go through it successfully till the Clone Calling step. However, I run into an error at the Lineage and Network Visualization step for which the input Celltag data should be Nx3 matrix. Since I only have results for V1, how should I proceed at this step?

sam-morris commented 2 years ago

With only the V1 library, it is a clonal analysis - lineage analysis cannot be performed without sequential barcoding using the V2 and V3 libraries.