Epigenetics & ChromatinBioinformaticsPeer-reviewed journal article
BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks
Lőrinc Sándor PongoriD, Jacob GrossiD, Roberto Vera AlvareziD, Junko MuraiiD, Sang‐Min Jang, Hongliang ZhangiD, Christophe E. RedoniD, Haiqing FuiD, Shar-Yin Naomi HuangiD, Bhushan L. ThakuriD, Adrian M. BarisiD, Leonardo Mariño‐RamíreziD, David LandsmaniD, Mirit I. AladjemiD, Yves G. PommieriD
Abstract
BAMscale is a one-step tool that processes DNA sequencing datasets from chromatin binding (ChIP-seq) and chromatin state changes (ATAC-seq, END-seq) experiments to DNA replication data (OK-seq, NS-seq and replication timing). The outputs include normalized peak scores in text format and scaled coverage tracks (BigWig) which are directly accessible to data visualization programs. BAMscale (available at https://github.com/ncbi/BAMscale) effectively processes large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools.
- assay: ChIP-seq
- assay: ATAC-seq
- assay: DNA methylation
- research focus: variant calling
- research focus: variant effect prediction
- approach: experimental assay
- Citations
- 66
- FWCI
- 2.59
- Field percentile
- top 9%
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