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Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

T. Hashimoto, M. J.L. de Hoon, S. M. Grimmond, C. O. Daub, Y. Hayashizaki, G. J. Faulkner
2009 Bioinformatics  
Here, we present MuMRescueLite, a low-resource requirement version of the MuMRescue software that has been used by several next generation sequencing projects to probabilistically reincorporate multi-mapping  ...  tags into mapped short read data.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp438 pmid:19605420 fatcat:vsbkipdjzndcnhpywxh5qzap4e

Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq [chapter]

Andrew B. Conley, I. King Jordan
2010 Msphere  
Here, we describe a simple pipeline method for using data generated through ChIP-seq to identify TE-derived TFBS.  ...  ChIP-seq has become a very popular and effective method for identifying in vivo DNA-protein interactions, such as those seen at transcription factor binding sites (TFBS), and has been used to show that  ...  Massively parallel sequencers generate millions of reads in run of a ChIP-seq experiment.  ... 
doi:10.1007/978-1-60761-854-6_14 pmid:20827595 fatcat:k2iefmdu2fhyjfzk7toupg7zsa

Characterization of microRNA-mediated cleavage events in Arabidopsis embryos

Aleksandra Plotnikova
2021 unpublished
We used fluorescent protein-based methods to determine the activity patterns of these miRNAs at cellular resolution during embryogenesis.  ...  Our nanoPARE data, together with transcriptome analysis of wild-type and miRNA-deficient embryos, enabled the identification of several miRNA families that cleave and repress distinct sets of transcription  ...  Further author contributions are listed in section 5.7 on page 35.  ... 
doi:10.25365/thesis.65899 fatcat:2tug4yd2ifdvhmjexyxodojlpa

Differential Gene Expression of Dorsal Pictorial Ornaments and Pigmentation in Skates (Rajidae, Chondrichthyes)

Alice Ferrari
To this end, the transcriptome profiling of different skin tissues was performed using the Illumina platform, whereas longer sequencing data were obtained from R. miraletus multiple organs using the Ion  ...  been used in parallel adaptations to similar environments and to understand if these traits follow species divergence or hybridisation.  ...  Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. Bioinformatics, 25(19), 2613-2614. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D.  ... 
doi:10.6092/unibo/amsdottorato/8191 fatcat:a5iipc3fzjd75af2flrudexenq