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BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

By Lorinc S Pongor, Jacob M Gross, Roberto Vera Alvarez, Junko Murai, Sang-Min Jang, Hongliang Zhang, Christophe Redon, Haiqing Fu, Shar-Yin Huang, Bhushan Thakur, Adrian Baris, Leonardo Marino-Ramirez, David Landsman, Mirit I. Aladjem, Yves Pommier

Posted 13 Jun 2019
bioRxiv DOI: 10.1101/669275

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.

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