Sep 7, 2016

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

Bioinformatics
Abhinav NelloreBen Langmead

Abstract

RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it requires extra work to obtain analysis products that incorporate data from across samples. We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. We use Rail-RNA to align 667 RNA-seq samples from the GEUVADIS project on Amazon Web Services in under 16 h for US$0.91 per sample. Rail-RNA outputs alignments in SAM/BAM format; but it also outputs (i) base-level coverage bigWigs for each sample; (ii) coverage bigWigs encoding normalized mean and median coverages at each base across samples analyzed; and (iii) exon-exon splice junctions and indels (features) in columnar formats that juxtapose coverages in samples in which a given feature is found. Supplementary outputs are ready for use with downstream packages for reproducible statistical analysis. We use Rail-RNA to identify exp...Continue Reading

  • References42
  • Citations8

References

Mentioned in this Paper

Computer Software
Patterns
Exons
Sequence Determinations, RNA
Splice Variants, Protein
Bio-Informatics
Computer Programs and Programming
Nuclear mRNA Cis Splicing, via Spliceosome
RNA Splicing
Systolic Anterior Movement of Mitral Valve

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