General

• 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

• 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?
• Can I run samples with low cell viability for ATAC or Multiome assays?
• Do I need to dissociate tissues into single cells first before isolating nuclei, or can I isolate nuclei directly from the whole tissue?

See all 7 articles

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?

Software

• [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?
• What annotations are included in the downloadable reference genomes for Cell Ranger ATAC?

See all 8 articles