It is fair to say that the new year has began with a bang for methods for RNA-seq analysis. Three new papers on new methods analyzing RNA-seq data have been published in the last month or so. And guess what, not so surprisingly all of the papers have Johns Hopkins University connection :-). yes, Steven Salzberg is part of all the papers with members from Ben Langsmead and Jeff Leek’s group.
The three papers kind of replaces earlier tools from Salzberg’s group (Bowtie/TopHat,Cufflinks, and Cuffmerge) the offer a totally new way to go from raw RNA-seq reads to differential expression analysis
- align RNA-seq reads to genome (HISAT instead of Bowtie/TopHat, STAR),
- assemble transcripts and estimate expression (StringTie instead of Cufflinks), and
- perform differential expression analysis (Ballgown instead of Cuffmerge).
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts), is a fast splice-aware aligner with low memory footprint just came out in Nature Methods. An earlier version of manuscript has been on bioRxiv since December. The HISAT software is available here at http://ccb.jhu.edu/software/hisat/index.shtml
- HISAT: a fast spliced aligner with low memory requirements by Daehwan Kim, Ben Langmead & Steven L Salzberg, Nature Methods
— nextgenseek (@nextgenseek) March 11, 2015
StringTie is a new fast and efficient reference based transcriptome assembler using RNA-Seq reads. StringTie uses network flow algorithm to assemble transcripts and it also estimates transcript expression. StringTie software is available at http://ccb.jhu.edu/software/stringtie/
- StringTie enables improved reconstruction of a transcriptome from RNA-seq reads by Mihaela Pertea,Geo M Pertea, Corina M Antonescu,Tsung-Cheng Chang,Joshua T Mendell & Steven L Salzberg
— nextgenseek (@nextgenseek) February 18, 2015
Ballgown allows to do estimation of differential expression of genes, transcripts, or exons from RNA seq experiments and more. Ballgown has out been out there for a while and its preprint was first available in bioRxiv last year. Ballgown software is available at https://github.com/alyssafrazee/ballgown.
- Ballgown bridges the gap between transcriptome assembly and expression analysis by Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg & Jeffrey T Leek