General

• What if I accidentally use the ATAC v1.1 protocol with ATAC v2 reagents?
• What cleanup steps are compatible with my ATAC sample?
• How do I remove granulocytes from my sample for standalone ATAC or Multiome assays?
• How do granulocytes affect my ATAC (standalone or Multiome) data?

Sample Prep - Nuclei

• What is the highest spin speed and spin time recommended for nuclei isolation for Single Cell ATAC or Single Cell Multiome assays?
• Is there a nuclei isolation protocol for ATAC in plants?
• I'm having trouble accurately counting nuclei. What can I do?
• Can I sort nuclei for Single Cell ATAC sequencing or Single Cell Multiome ATAC + GEX?
• How do I perform a lysis timeline to optimize my nuclei isolation for Single Cell ATAC sequencing?
• How can I optimize my nuclei prep for Single Cell ATAC sequencing?

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Transposition

• Can whole cells be used as input into the transposition reaction?

Library Construction

• My ATAC trace looks different, is it ok to proceed?
• Why does my ATAC trace only have 1 peak?
• What are the peaks present in my ATAC library trace?

Sequencing

• Can I do a shallow sequencing run to QC my ATAC sample?
• Can I sequence Single Cell ATAC libraries with other libraries?
• Can I change the sequencing read length of R1N and R2N?
• Can I change the sequencing read lengths of the i5 and i7 indices for ATAC libraries?

Software

• Does cellranger-atac aggr redo peak calling?
• [error] Entry 0 in sample_defs are missing input FASTQs
• In scATAC-seq, how are the z-scores for transcription factor motif enrichment calculated?
• How can I convert the peak-barcode matrix from Cell Ranger ATAC 1.x to a CSV file?
• How do I calculate median number of peaks per cell for Cell Ranger ATAC?
• Does the Cell Ranger ATAC pipeline use static thresholds to call peaks and identify cell barcodes?

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