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LiBiNorm : an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
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Dryer, Nigel P., Shahrazaie, Vahid and Hebenstreit, Daniel (2019) LiBiNorm : an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ, 7 . e6222. doi:10.7717/peerj.6222 ISSN 2167-8359.
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Official URL: https://doi.org/10.7717/peerj.6222
Abstract
Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics | |||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| Library of Congress Subject Headings (LCSH): | Gene expression, Nucleotide sequence | |||||||||
| Journal or Publication Title: | PeerJ | |||||||||
| Publisher: | PeerJ, Ltd. | |||||||||
| ISSN: | 2167-8359 | |||||||||
| Official Date: | 4 February 2019 | |||||||||
| Dates: |
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| Volume: | 7 | |||||||||
| Article Number: | e6222 | |||||||||
| DOI: | 10.7717/peerj.6222 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Copyright Holders: | 2019 Dyer et al. | |||||||||
| Date of first compliant deposit: | 7 December 2018 | |||||||||
| Date of first compliant Open Access: | 14 February 2019 | |||||||||
| RIOXX Funder/Project Grant: |
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