- Unique identifier:
- Command line interface
- Input data:
- A list of genomic coordinates of low complexity regions in BED or BAM format.
- Operating system:
- Computer skills:
- Software type:
- Restrictions to use:
- Output data:
- A cleaned BAM file with reads overlapping low complexity regions at a given threshold filtered out, the filtering statistics.
- GNU General Public License version 3.0
- Mikhail Dozmorov <>
No open topic.
(Dozmorov et al., 2015)
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.
PMID: 26423047 DOI: 10.1186/1471-2105-16-S13-S10
Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA; Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
This work was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (a subaward from grant # P30 AR053483), by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences (a subaward from grant # P30GM103510), by the National Center for Advancing Translational Sciences (CTSA award No. UL1TR000058), by NIH/NIGMS (P30GM110766, P20GM103456, P20GM103636), by NIH/NIAMS (R01AR065953, P50AR060804), and by the National Science Foundation division of Advanced CyberInfrastructure # ACI-1345426.
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