---
id: "claim:universal-preprocessing-of-single-cell-genomics-data-2023-09-15-biorxiv:977589cbd7736e145279"
kind: "claim"
title: "Controlling preprocessing implicates an experimental source for the tag-efficiency difference."
description: ""
url: "https://sina.bio/claim/controlling-preprocessing-implicates-an-experimental-source-for-the-tag-a5b8f24f"
---

# Controlling preprocessing implicates an experimental source for the tag-efficiency difference.

## Content

Controlling preprocessing implicates an experimental source for the tag-efficiency difference.

## Metadata

```json
{
  "claim_position": 69,
  "source_publication_id": "version:universal-preprocessing-of-single-cell-genomics-data--2023-09-15-biorxiv",
  "source_work_id": "work:universal-preprocessing-of-single-cell-genomics-data"
}
```

## Connections (2)

### Universal preprocessing of single-cell genomics data

- ID: `version:universal-preprocessing-of-single-cell-genomics-data--2023-09-15-biorxiv`
- Kind: `publication`
- Direction: `incoming`
- URL: <https://sina.bio/publication/universal-preprocessing-of-single-cell-genomics-data>

This publication contains this grounded claim.

> Uniform preprocessing makes it straightforward to compare modalities within the same technology. Figure 2 shows a comparison of data from three different DOGMA-seq (Mimitou et al. 2021) modalities as assayed in (Z. Xu et al. 2022), all preprocessed with cellatlas and the tools it uses: snATAK, kallisto bustools, and kITE. Uniform preprocessing also allows for quantifying the efficiency of assaying the different modalities. The fact that the RNA and protein libraries have a similar number of UMIs captured for a given number of reads (Figure 2a,b) is consistent with similar dilutions of the libraries (1.99nM and 2.2nM respectively), whereas the tag library efficiency (Figure 2c) is distinctly different, likely as a result of dilution to 0.27nM. While the exact cause for the difference requires further investigation, the control for preprocessing that cellatlas provides points to an experimental cause for the difference. Uniform preprocessing also provides a direct comparison of the distinct modalities in terms of their detection efficiency (Figures 2d,e,f). The protein detection saturates because DOGMA-seq protein modality only assayed 163 proteins. The discrepancy between cells in which protein is detected but not ATAC peaks, versus those in which protein is detected but not RNA, is interesting and warrants further investigation.

Source: 2023-09-15-biorxiv.pdf — <https://sina.bio/source/2023-09-15-biorxiv-pdf>

### Uniform DOGMA-seq preprocessing showed similar RNA and protein UMI efficiency, different tag-library efficiency, and an

- ID: `result:universal-preprocessing-of-single-cell-genomics-data-2023-09-15-biorxiv:654f149a358489407598`
- Kind: `result`
- Direction: `incoming`
- URL: <https://sina.bio/result/uniform-dogma-seq-preprocessing-showed-similar-rna-and-protein-umi-effi-6bb90c9f>

This claim supports this result.