Rail-RNA – Scalable analysis of RNA-seq splicing and coverage

RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. A source of frustration for investigators analyzing a given dataset is the inability to rapidly and reproducibly align its samples jointly. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it is difficult to reproduce the exact analysis without access to original computing resources.

Researchers at Johns Hopkins University have developed 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. They have used Rail-RNA to align 666 RNA-seq samples from the GEUVADIS project on Amazon Web Services in 12 hours for US$0.69 per sample. Rail-RNA produces alignments and base-resolution bigWig coverage files, ready for use with downstream packages for reproducible statistical analysis. The researchers identified 290,416 expressed regions in the GEUVADIS samples, including 21,224 that map to intergenic sequence.

rna-seqRail-RNA eliminates redundant alignment work by rst aggregating reads by nucleotide sequence and, where appropriate, aligning only unique read sequences to the genome.

Availability – Rail-RNA is open-source software available at http://rail.bio

Nellore A , Collado-Torres L , Jaffe AE , Morton J , Pritt J , Alquicira-Hernández J Leek JT , Langmead B. (2015) Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. bioXriv [abstact]

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