• Subscribe to the RNA-Seq Blog

  
  

  
  Or subscribe by RSS Reader
  
• 5,976 feed subscribers
• 
  

• Featured Events

  

• 

• 

• Media Partners

  
  

• 

• Polls

  How long have you been involved with RNA Sequencing?

  • Just now learning about RNA-Seq
  • less 1 year
  • more than 1 year
  • more than 2 years
  • more than 3 years
  • more than 4 years
  • more than 5 years

  View Results

   Loading ...
• Search for:

• Data Analysis Tools

  Transcriptome Assembly Tools

  Expression & Quantification

  Unpliced Mapping Tools

  Splicing and Junction Mapping

  Analysis Pipelines

  Clouding Platforms

  Databases

  Other Tools

• Tag Cloud

  allele-specific expression alternative splicing bioconductor bioinformatics breast cancer broad institute chip-seq cloud computing cufflinks Data Analysis data analysis pipeline deep sequencing de novo assembly differential expression encode ensembl expression analysis galaxy gene expression high-throughput sequencing illumina ion torrent junction mapping library preparation life technologies lncrna microarray microarrays microrna mirna next-generation sequencing next-gen sequencing pacific biosciences poll results RNA-Seq rnaseq rna sequencing roche tophat transcriptome transcriptome analysis transcriptome assembly transcriptomes transcriptome sequencing transcriptomics

  WP Cumulus Flash tag cloud by Roy Tanck requires Flash Player 9 or better.

• Categories

  Select Category Advertisers Analysis Pipelines Annotation Clouding Platforms Controls Data Analysis Data Analysis Data Sets Databases Events Expression and Quantification Grants / Funding Industry News Information Jobs Library Preparation Methods News Other Tools Patents Pathway Analysis Poll Results Presentations Press Release Publications Reader Conributions Request for RNA-Seq Services Review Sequencing Protocols SNP Detection Splicing and Junction Mapping Statistical Analysis Transcriptome Assembly Tools Transcriptome Sequenced Uncategorized Unspliced Mapping Tools Web Tools Workflow
• 
  
  

• Recent Comments

  • Brian Haas on Interview – Brian Haas Manager of Genome Annotation, Outreach, Bioinformatics and Analysis Broad Institute
  • Bret on The Magic of RNA-Seq
  • Bob Copeman on RobiNA – a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
  • Oz Solomon on Expression Analysis Announces 2013 Grant Program
  • Dr. Jayakishan Meher on Bioinformatics postdoctoral research fellowship available

• Popular Search Terms

  • grape
  • tirthadipa pradhan
  • rna seq analysis
  • rna-seq analysis
  • next generation sequencing ppt
  • rna seq data analysis
  • rna seq vs microarray
  • wine grapes
  • RSEM
  • mangrove

• Recent Search Terms

  • performance evaluation of alignment algorithm rna seq
  • transcriptome analysis review
  • pacific biosciences layoff
  • price kit truseq stranded rna
  • transcriptomics analysis methods
  • glalaxy DNAseq
  • tagging method for transcriptome
  • rna sequence hexamers
  • url shortener
  • rna sequencing aberrant splicing

• Archives

  • May 2013
  • April 2013
  • March 2013
  • February 2013
  • January 2013
  • December 2012
  • November 2012
  • October 2012
  • September 2012
  • August 2012
  • July 2012
  • June 2012
  • May 2012
  • April 2012
  • March 2012
  • February 2012
  • January 2012
  • December 2011
  • November 2011
  • October 2011
  • September 2011
  • August 2011
  • July 2011
  • June 2011
  • May 2011
  • April 2011
  • March 2011
  • February 2011
  • January 2011
  • December 2010
  • November 2010
  • October 2010
  • September 2010
  • August 2010
  • July 2010
  • June 2010
  • May 2010
  • April 2010
  • February 2010
  • January 2010
  • January 2009

The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species.

Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.

• Su AAH, Tripp V, Randau L. (2013) RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri NAR [Epub ahead of print]. [article]

Incoming search terms:

• fruits tropicaux pine apple
• transcriptome profiling of giardia intestinalis using strand-specific rna-se
• cummbund
• halophytes plants adaptation
• sequence rna seq
• stress tolerance rnaseq population genomics
• tcga rnaseq depth
• trna cancer
• xrtyacfsgimrq

MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a destructive pest of wheat and model organism for studying gall midge biology and insect – host plant interactions.

In this study, researchers from the Department of Entomology, Kansas State University systematically analyzed miRNAs from the Hessian fly. Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species. A genome-wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Analysis of the 611 putative genes revealed a striking feature: the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes.

The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior. The dramatic expansion of identical or similar miRNAs provides a unique system to study functional relations among miRNA iso-genes as well as changes in sequence specificity due to small changes in miRNAs and in their mRNA targets. These results may also facilitate the identification of miRNA genes for potential pest control through transgenic approaches.

• Khajuria C, Williams CE, El Bouhssini M, Whitworth RJ, Richards S, Stuart JJ, Chen MS. (2013) Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor. BMC Genomics 14:187. [article]

Incoming search terms:

• mirdeep pair-end small RNA SEQ
• transcriptome analysis using rna-seq in insect pests
• how to find transgenic gene expression in rnaseq data
• lowess normalization microrna seq
• methanol utilization pathway
• mirna normalization miRNA-seq
• mirna seq quality report
• rna-seq transgenic plants

Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E.

Now, researchers at the Karolinska Institutet, Sweden have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-Seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-Seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3′ UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology.

Franzén O, Jerlström-Hultqvist J, Einarsson E, Ankarklev J, Ferella M, Andersson B, Svärd SG. (2013) Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq. PLoS Comput Biol 9(3), e1003000. [article]

Incoming search terms:

• seed transcriptome torrent
• rna-seq wheat tolerance
• rna-seq asthma
• ppt RNA transcriptome
• transcriptomes sequenced
• understanding transcriptomes
• Ananas comosus RNAseq
• tcga rna seq depth
• tcga rna-seq 100 million
• t cell subpopulations and rna-seq

Populus euphratica, a typical hydro-halophyte, is ideal for studying salt stress responses in woody plants. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that fulfilled an important post-transcriptional regulatory function. MiRNA may regulate tolerance to salt stress but this has not been widely studied in P. euphratica.

In this investigation, the small RNAome, degradome and transcriptome were studied in salt stress treated P. euphratica by deep sequencing. Two hundred and eleven conserved miRNAs between Populus trichocarpa and P. euphratica have been found. In addition, 162 new miRNAs, belonging to 93 families, were identified in P. euphratica. Degradome sequencing experimentally verified 112 targets that belonged to 51 identified miRNAs, few of which were known previously in P. euphratica. Transcriptome profiling showed that expression of 15 miRNA-target pairs displayed reverse changing pattern under salt stress.

Together, these results indicate that, in P. euphratica under salt stress, a large number of new miRNAs could be discovered, and both known and new miRNA were functionally cleaving to their target mRNA. Expression of miRNA and target were correspondingly induced by salt stress but that it was a complex process in P. euphratica.

• Li B, Duan H, Li J, Deng XW, Yin W, Xia X. (2013) Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol [Epub ahead of print]. [abstract]

Incoming search terms:

• RNA-seq populus
• rna seq populus
• degradome or rna-seq
• rnaseq drosophila immunity
• rna-seq transcriptome
• rna and small rna transcriptome profile
• populus trichocarpa degradome
• populus euphratica
• populus degradome sequencing
• pgm library preparation micro rna

from GenomeWeb News

NEW YORK (GenomeWeb News) – Worker wasps have a more active transcriptome than queen wasps do, Seirian Sumner, a senior lecturer at the University of Bristol, and her colleagues reported in Genome Biology yesterday.

Workers, queens, and other social wasp castes share the same genome, but how that genome leads to alternative phenotypes like workers and queens is not fully known, especially as social wasps, and other social insects, are derived from non-social, solitary ancestors. In social wasps, queen wasps are responsibly mainly for reproduction while workers care for the offspring. Read more

Incoming search terms:

• Freq-seq
• illumina mapper
• RNAseq Illumina Technology - workshop
• transcriptome phylogeny
• does truseq rna introduce duplicates
• domesticat crop rna-seq
• social behaviour in wasp
• Social behavior in wasps
• smarter rnaseq bias
• library prep miseq rna-seq

The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, researchers at South China Agricultural University, Guangzhou applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.).

The researchers have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. They obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Their results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations.

These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, this strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.

• Liu S, Li W, Wu Y, Chen C, Lei J. (2013) De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids. PLoS One 8(1), e48156. [article]

Incoming search terms:

• RNA-seq strategy
• RNA seq de novo
• asia kuczek
• chili pepper lncRNA
• unigene annotation rna-seq and clc bio
• unigenes using trinity assembler

Scientists at Raffaele Scientific Institute, Italy report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report they show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5′/3′ UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%), terminator consensus motifs for 22 sRNAs (8.5%), and both motifs for 35 sRNAs (14%). Additionally, 20/23 candidates were visualized by Northern blot analysis and 5′ end mapping by primer extension confirmed the RNA-seq data.

Additionally, the researchers used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. They found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.

• Miotto P, Forti F, Ambrosi A, Pellin D, Veiga DF, Balazsi G, Gennaro ML, Di Serio C, Ghisotti D, Cirillo DM. (2012) Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. PLoS One 7(12), e51950. [article]

Incoming search terms:

• mirauto small rna
• rna seq mycobacterium
• tb rnaseq

Scientists at the South China University of Technology used a massively parallel mRNA sequencing platform (RNA-Seq), based on next-generation sequencing technology, to map and quantify the dynamic transcriptome of Pichia pastoris (a widely used as a bioengineering platform for producing industrial and biopharmaceutical proteins ) at the genome scale under growth conditions with glycerol and methanol as substrates. The results describe the transcription landscape at the whole-genome level and provide annotated transcript structures, including untranslated regions (UTRs), alternative splicing (AS) events, novel transcripts, new exons, alternative upstream initiation codons (uATGs), and upstream open reading frames (uORFs). Internal ribosome entry sites (IRESs) were first identified within the UTRs of genes from P. pastoris, encoding kinases and the proteins involved in the control of growth. They also provide a transcriptional regulation model for P. pastoris grown on different carbon sources.

The researchers suggest that the IRES-dependent translation initiation mechanism also exists in P. pastoris. Retained introns (RI) are determined as the main AS event and are produced predominantly by an intron definition (ID) mechanism.

These results describe the metabolic characteristics of P. pastoris with heterologous protein production under methanol induction and provide rich information for further in-depth studies of P. pastoris protein expression and secretion mechanisms.

• Liang S, Wang B, Pan L, Ye Y, He M, Han S, Zheng S, Wang X, Lin Y. Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. BMC Genomics 13(1), 738. [abstract]

Incoming search terms:

• pichia pastoris
• pichia pastoris metabolism
• heme pathway pichia
• heme pichia
• mechanism of pichia pastoris
• microrna pichia pastoris ptt
• pichia expression workflow
• pichia metabolism
• pichia pastoris 2012 ppt

Bud dormancy is a critical developmental process that allows perennial plants to survive unfavorable environmental conditions. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms regulating bud dormancy in this species are unknown. Because genomic information for pear is currently unavailable, transcriptome and digital gene expression data for this species would be valuable resources to better understand the molecular and biological mechanisms regulating its bud dormancy. Read more

Incoming search terms:

• pear
• fruit tree of the world
• pear dormancy next generation seuqncing china
• Suli pear pyrus pyrifolia white pear group
• transcriptomic analysis of pear

The deep sequencing of an mRNA population, RNA-seq, is a very successful application of next-generation sequencing technologies (NGSTs). RNA-seq takes advantage of two key NGST features: (1) samples can be mixtures of different DNA pieces, and (2) sequencing provides both qualitative and quantitative information about each DNA piece analyzed.

A team led by researchers at Vanderbilt University recently used RNA-seq to study the transcriptome of Aspergillus fumigatus, a deadly human fungal pathogen. Analysis of the RNA-seq data indicates that there are likely tens of unannotated and hundreds of novel genes in the A. fumigatus transcriptome, mostly encoding for small proteins. Inspection of transcriptome-wide variation between two isolates reveals thousands of single nucleotide polymorphisms. Finally, comparison of the transcriptome profiles of one isolate in two different growth conditions identified thousands of differentially expressed genes. These results demonstrate the utility and potential of RNA-seq for functional genomics studies in A. fumigatus and other fungal human pathogens.

• Rokas A, Gibbons JG, Zhou X, Beauvais A, Latgé JP. (2012) The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Ann N Y Acad Sci 1273(1), 25-34. [abstract]

Incoming search terms:

• cho microarray
• transcriptome sequencing application PPT

Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases.

Now researchers at Universiti Malaysia Sabah have performed RNA-Seq of ripe yellow pineapple fruit flesh using Illumina RNA sequencing technology. About 4.7 million paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown.

• Ong WD, Voo LY, Kumar VS. (2012) De Novo Assembly, Characterization and Functional Annotation of Pineapple Fruit Transcriptome through Massively Parallel Sequencing. PLoS One 7(10), e46937. [article]

Incoming search terms:

• nanas
• ananas fruit
• pineapple fruit
• ananas
• Ananas comosus RNA
• fruit pineapple
• pineapple fruit texture

Barley (Hordeum vulgare L.) is among the world’s earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here, the International Barley Genome Sequencing Consortium presents an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. They developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 ‘high-confidence’ genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Their data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

• The International Barley Genome Sequencing Consortium. (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature [Epub ahead of print]. [article]

Incoming search terms:

• differential rna sequencing
• barley rna-seq
• DNA sequence assembly

Bamboo occupies an important phylogenetic node in the grass family with remarkable sizes, woodiness and a striking life history. However, limited genetic research has focused on bamboo partially because of the lack of genomic resources.  Now, a team led by researchers at the Chinese Academy of Forestry in Beijing performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset for the Ma bamboo (Dendrocalamus latiflorus Munro). Read more

Incoming search terms:

• Japanese macaque eating a crab
• big node bamboo
• de novo assembly bamboo

Next Page →

• 

• 

• 

• 

• Social Networking Pages

  

• 

• SEQanswers – RNA Sequencing

  • standard of clean data May 21, 2013
    Hi 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, 2013
    Hi 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, 2013
    Hi, 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, 2013
    Hi, 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, 2013
    Hi, 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, 2013
    Hi, We use RNA isolation and library preparation protocols which capture polyadenylated RNA. My question is what kinds of RNA can we expect to... […]
    Kocur

• 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 expression
    I 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 TopHat
    Which 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. […]