Application to Bulk ATAC-seq

[Emily Lachtara]

Hello,

I am interested in applying Cicero to bulk ATAC-seq data.  I want to avoid the aggregation of cells step (no need for this in bulk). Is there away around this step in the pipeline, and if possible could you share the code to apply Cicero to bulk?

Best,

Emily

[hpl...@gmail.com]

Hello,

Cicero wasn't designed for use in bulk ATAC-seq, and I would not expect it to work unless you had very many bulk samples. If you did want to attempt it, you would need to skip the make_cicero_cds step and generate a CDS object using bulk samples as the 'cells'.

Best,

Hannah