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RNAtor: an Android-based application for biologists to plan RNA sequencing experiments

Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda
doi: https://doi.org/10.1101/095315
Shruti Kane
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore
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Himanshu Garg
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore
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Neeraja M. Krishnan
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore
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Aditya Singh
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore
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Binay Panda
1Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore
2Strand Life Sciences, Bangalore 560024, India
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  • For correspondence: binay@ganitlabs.in
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Abstract

RNA sequencing (RNA-seq) is a powerful technology for identification of novel transcripts (coding, non-coding and splice variants), understanding of transcript structures and estimation of gene and/or allelic expression. There are specific challenges that biologists face in determining the number of replicates to use, total number of sequencing reads to generate for detecting marginally differentially expressed transcripts and the number of lanes in a sequencing flow cell to use for the production of right amount of information. Although past studies attempted answering some of these questions, there is a lack of accessible and biologist-friendly mobile applications to answer these questions. Keeping this in mind, we have developed RNAtor, a mobile application for Android platforms, to aid biologists in correctly designing their RNA-seq experiments. The recommendations from RNAtor are based on simulations and real data.

Availability and Implementation The Android version of RNAtor is available on Google Play Store and the code from GitHub (https://github.com/binaypanda/RNAtor).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 19, 2016.
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RNAtor: an Android-based application for biologists to plan RNA sequencing experiments
Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda
bioRxiv 095315; doi: https://doi.org/10.1101/095315
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RNAtor: an Android-based application for biologists to plan RNA sequencing experiments
Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda
bioRxiv 095315; doi: https://doi.org/10.1101/095315

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