Sample Prep - Nuclei

• Can I sort nuclei for Single Cell ATAC sequencing?
• 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?
• How can I assess the quality of my nuclei for Single Cell ATAC Sequencing?
• Can I run samples with low cell viability?
• I want to perform both Single Cell ATAC and Gene Expression profiling, which sample preparation protocol should I use?

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Transposition

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

Library Construction

• 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

• 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?
• How can I compare scATAC and scRNA-seq data from the same biological sample?
• 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?

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