TopHat is a fast splice junction mapper for RNA-Seq reads.
A fast splice junction mapper for RNA-seq reads that uses bowtie (see above)
s a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read al...
edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq...
标签：RNA-Seq, RNA-Seq Quantitation,ChIP-Seq, Gene Expression Analysis, DNA methylation
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support ...
标签：RNA-Seq Alignment, RNA-Seq Quantitation, Alternative Splicing, Transcriptome, RNA-Seq
DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).
Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.
标签：Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program al...
We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the res...
Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to i...
An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.
We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent...