Subscribe to the RNA-Seq Blog
Featured Events
.png)
Media Partners
Polls
Loading ...
Jan
1
SpliceMap – a de novo splice junction discovery tool
Filed Under Splicing and Junction Mapping | Leave a Comment
Alternative splicing is a prevalent post-transcriptional process, which is not only important to normal cellular function but is also involved in human diseases. The newly developed second generation sequencing technique provides high-throughput data (RNA-seq data) to study alternative splicing events in different types of cells. Read more
Incoming search terms:
- splicemap
- find alternative splices for Trinity assembly output
- alternative splicing assembler
- splicemap tophat
- Splicemap assembly
- splicemap 454
- junction support fpkm
- de novo alternative splice prediction
- computational de novo splicing
- alternative splicing de novo prediction
Sep
1
New Splice Junction Mapping Tool – MapSplice
Filed Under Splicing and Junction Mapping | Leave a Comment
The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. Here is 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. Read more
Incoming search terms:
- mapsplice
- splice junction mapping
- rna-seq junction map
- junction read rnaseq
- splicing rna tool
- splicing analysis tools
- spliced mapping of reads
- splice junction analysis
- rnaseq read span junction
- rna-seq splicing tools
Jul
9
RNA-Seq Web Resources
Filed Under Data Analysis | Leave a Comment
Technical Guides
- RNA-Seq Technical Guide – From Genomeweb. A panel of experts answer questions regarding RNA-Seq experiments.
Discussion Forums
- The RNA-Seq Blog – A discussion forum for all things transcriptomic.
- SEQanswers – The next-generation sequencing community – threads tagged with RNA-Seq.
Webinars
- An Illumina-Demonstrated Method for Sequencing the Complete Transcriptome - Session will introduce an improved solution for the reduction of abundant transcripts in RNA-Seq experiments, based on an Illumina-optimized protocol utilizing duplex-specific nuclease (DSN) from Evrogen. Illumina scientists will provide a brief overview of DSN, will describe the enhancements made to the DSN workflow to optimize its performance for Illumina RNA-Seq, and will demonstrate its utility in a wide range of applications, including ncRNA discovery and FFPE transcriptome profiling.
RNA-Seq Data Analysis Tools
- rQuant.web – is a web service to provide convenient access to tools for the quantitative analysis of RNA-Seq data. It allows to determine abundances of multiple transcripts per gene locus from RNA-Seq measurements. rQuant.web is available free of charge, to all users as a tool in a Galaxy installation.
- Scripture – is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.
- Cufflinks – assembles transcripts, estimates their abundances, and tests for differential expression and regulation 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 each one.
- SpliceMap – SpliceMap is a de novo splice junction discovery tool. It offers high sensitivity and support for arbitrarily long RNA-seq read lengths.
- TopHat – is 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 aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
- PALMapper – a combination of the spliced alignment method QPALMA with the short read alignment tool GenomeMapper. The resulting method, called PALMapper, efficiently computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
- RNA-MATE – A recursive mapping strategy for high-throughput RNA-sequencing data.
- ERANGE – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
- SeqMap – A Tool For Mapping Millions Of Short Sequences To The Genome.
- Bioconductor – Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
- BWA – BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (targe), such as the human reference genome.
- CisGenome – An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
- GenePattern – is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
- Galaxy – Mapping pipeline for Illumina, 454, and SOLiD sequencing data.
- MAQ – stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
- UCSC Genome Browser – This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.
Incoming search terms:
- seq web
- rquant
- chip-seq fastqc to cisgenome
- s eq uen
- RNA-seq websites
- rna seq questions
- rna seq question
- resource for learning rna seq
- mtdna rna-seq seq answers
- cisgenome protocol
Jun
18
RNA-Seq Data Analysis Tools
Filed Under Data Analysis | 2 Comments
- Scripture – is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.
- Cufflinks – assembles transcripts, estimates their abundances, and tests for differential expression and regulation 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 each one.
- SpliceMap – SpliceMap is a de novo splice junction discovery tool. It offers high sensitivity and support for arbitrarily long RNA-seq read lengths.
- TopHat – is 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 aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
- PALMapper – a combination of the spliced alignment method QPALMA with the short read alignment tool GenomeMapper. The resulting method, called PALMapper, efficiently computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
- RNA-MATE – A recursive mapping strategy for high-throughput RNA-sequencing data.
- ERANGE – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
- SeqMap – A Tool For Mapping Millions Of Short Sequences To The Genome.
- Bioconductor – Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
- BWA – BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (targe), such as the human reference genome.
- CisGenome – An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
- GenePattern – is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
- Galaxy – Mapping pipeline for Illumina, 454, and SOLiD sequencing data.
- MAQ – stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
- UCSC Genome Browser – This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.
Incoming search terms:
- rna seq analysis
- rna-seq analysis
- rna seq data analysis
- rnaseq analysis
- rna-seq pipeline
- rna seq analysis software
- RNA-seq data analysis
- rna seq data analysis pipeline
- rna seq data
- rnaseq pipeline
Social Networking Pages
-
SEQanswers – RNA Sequencing- standard of clean data May 21, 2013Hi all I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as... […]Pengfei Liu
- Problem with cummeRbund diffData() May 20, 2013Hi all, I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with... […]Enrique Zudaire
- How to increase rowsize in heatmap? May 16, 2013Hi, I am a complete newbie to all things cummeRbund and am currently fighting with generating readable heatmaps. When I use ... […]Mags
- novoalign mapping May 15, 2013Hi, I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads I am new to novoalign(went through the... […]abh
- Design of expt across multiple lanes May 15, 2013Hi, I am performing an RNA-seq experiment to look at differential expression. The design is as follows: 2 populations x 3 biological... […]jbono
- RNA kinds expected in RNA-seq results May 15, 2013Hi, We use RNA isolation and library preparation protocols which capture polyadenylated RNA. My question is what kinds of RNA can we expect to... […]Kocur
- standard of clean data May 21, 2013
- Biostar – RNA-Seq
- How do TopHat options -g , --supress-hits, and Bowtie options interplay?Hi, I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now? I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments. Now, the description sounds mo […]
- What happened to -k in TopHat for multiple-mapping reads?Selecting -g n in tophat does not discard reads mapping more than n, but instead only reports n alignments for those out all all their TOP scoring alignments. I think there used to be an option -k that would allow one to discard reads that topped x alignments -- whatever happened to that? I only see -g in the tophat 2 manual, no reporting options like before […]
- Does tophat use the library-type information for mapping, or just for the XS flag?When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A tag, which is useful for subsequent analyses, such as annotation. However, does this information influence the "mappability" of reads, or is this unaffected? My guess is that the information will be considered for mapping […]
- Purpose of Y-shaped adapters in Illumina Sequencing?Hi all, Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. What are the advantages of this? My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that: -Upon primer a […]
- Cell Type composition in a tissue based on gene marker expressionI am not sure if the following would even make sense.... Tissues are composed of composite cell types, and often there are studies such as microarray/NGS where we perform a collective sampling of cells from these tissues. Information about the composition (say percentage of cell type) is not taken into consideration. In some case (such as brain/cancer), ther […]
- Which SNP caller / method to use after aligning RNA-seq with TopHatWhich SNP caller / method can / should I use after aligning RNA-seq data with TopHat? For genomic data I use GATK, but supposedly it is not just as easy as running GATK on the TopHat RNA-seq data. The team from Broad has no information / documentation on how to use GATK for RNA-seq data. I don't have any variants yet from DNA re-sequencing. […]
- How do TopHat options -g , --supress-hits, and Bowtie options interplay?