From 347b5e7f2a4c8b86f0c3759cc2722336965be672 Mon Sep 17 00:00:00 2001 From: Wuming Gong Date: Tue, 11 Apr 2023 13:02:18 -0500 Subject: [PATCH] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0bdafca..6799f6a 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Wuming Gong, Nikita Dsouza and Daniel J. Garry ## Abstract -Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data. SeATAC is available at https://github.com/gongx030/seatac as an R package. The preprint can be found at [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.04.25.489439v1). +Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data. SeATAC is available at https://github.com/gongx030/seatac as an R package. The preprint can be found at [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.04.25.489439v1). Additionally, SeATAC has been used to investigate how Etv2 shape the chromatin landscape in [MEF reprogramming](https://www.nature.com/articles/s41556-022-00901-3) and [limb development](https://www.nature.com/articles/s41467-022-31848-6). ## Main Figures