Reproducing ASAP-seq and DOGMA-seq analyses

Last updated: June 10, 2021

This repository contains all code needed to reproduce all analyses:

Scalable, multimodal profiling of chromatin accessibility, gene expression, and protein levels in single cells

Eleni P. Mimitou+, Caleb A. Lareau+, Kelvin Y. Chen+ et al. Scalable, multimodal profiling of chromatin accessibility, gene expression, and protein levels in single cells. Nature Biotechnology 2021. Online here

Setup

To best use this resource, we recommend pairing with large data files (that are not compatible with github as they exceed 100Mb). These files are available from the Open Science Framework.

Once one downloads the zip archieve from OSF (~48 Gb), place the extracted folder in the same directory as this repository named asap_large_data_files (as shown below). This will enable running custom code to reproduce items in the output folders.

.
├── asap_large_data_files
│   ├── CD4_stimulation_asapseq
│   ├── bonemarrow_data
│   ├── broad_experiment_pbmcs
│   ├── intraCD4_stimulation_asapseq
│   ├── multiome_pbmc_stim
│   ├── nygc_pbmc
│   ├── pbmc_stim_data
│   └── species_mix
└── asap_reproducibility
    ├── CD4_CRISPR_asapseq
    ├── README.md
    ├── bonemarow_asapseq
    ├── global_functions
    ├── intracellular_CD4_CRISPR_asapseq
    ├── intracellular_TBNK_asapseq
    ├── pbmc_TBNK_comparisons_asapseq
    ├── pbmc_stim_multiome
    ├── pbmc_stimulation_asapseq_citeseq
    └── species_mix_asapseq

The code assumes a relative file path with this organization.

Figure to directory mapping

Note this is for the version of the manuscript published in Nature Biotechnolgy and not the previous bioRxiv verison.

Figure 1 | species_mix_asapseq,pbmc_TBNK_comparisons_asapseq
Figure 2 | pbmc_TBNK_comparisons_asapseq
Figure 3 | bonemarow_asapseq
Figure 4 | pbmc_stimulation_asapseq_citeseq
Figure 5 | pbmc_stim_multiome
Figure 6 | CD4_CRISPR_asapseq
Figure 7 | intracellular_asapseq,intracellular_CD4_CRISPR_asapseq

Reformatting fastqs for process with kite

We use kite (part of kallisto|bustools) to do all of the ADT/HTO tag quantification.

Since the fastqs the come off the sequencer aren't currently supported by the kite workflow, we have this accessory script to convert fastq files into a format similar to the 10x 5p scRNA-seq. This way, these can be more rapdily quantified.

https://github.com/caleblareau/asap_to_kite

Questions/ contact

Formal questions about this work should be addressed to the corresponding author: Peter Smibert.

For questions or comments related to the specific code, please raise an issue or submit a pull request.