What question did this study set out to answer?

To develop a scalable, cloud-enabled spliced aligner capable of analyzing large-scale multi-sample RNA-seq datasets simultaneously to increase throughput and accuracy.

September 3, 2016BioinformaticsOpen Access

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

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Authors

ANAbhinav NelloreNYU Langone Health LCLeonardo Collado‐TorresL&S Consulting (South Africa)AJAndrew E. JaffeJohns Hopkins University

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Implication

Software evaluation study demonstrates cost-effective multi-sample RNA-seq spliced alignment across hundreds of human samples, highlighting scalable discovery of novel expressed regions.

Key Points

To develop a scalable, cloud-enabled spliced aligner capable of analyzing large-scale multi-sample RNA-seq datasets simultaneously to increase throughput and accuracy.
Engineered Rail-RNA, an open-source spliced aligner built for cloud computing architectures to eliminate redundant computations across pooled samples.
Evaluated computational efficiency and biological discovery by aligning 667 human RNA-seq samples from the GEUVADIS project on Amazon Web Services.
Aligned 667 RNA-seq samples on Amazon Web Services in under 16 hours at a computational cost of $0.91 per sample.
Demonstrated improved alignment accuracy relative to annotation-assisted aligners while outputting standard alignment files, sample-level and mean/median coverage bigWigs, and splice-junction tables.
Identified annotated and unannotated expressed regions that display consistent variation patterns across human populations and known confounding variables.

Cite This Study

Nellore et al. (2016) studied this question.

synapsesocial.com/papers/6a12bfbb86514ddae6c07b9a https://doi.org/10.1093/bioinformatics/btw575

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Implication

Software evaluation study demonstrates cost-effective multi-sample RNA-seq spliced alignment across hundreds of human samples, highlighting scalable discovery of novel expressed regions.

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

Discussion

Member takes

Implication

Key Points

Cite This Study

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

Discussion

Member takes

Implication

Key Points

Cite This Study

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