View Full Version : RNA Sequencing
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- RNA-seq with paired-end reads
- Erange
- mRNA preparation for RNA-Seq
- Why are the ends different in RNA seq?
- Abi Solid WT Sample Data vs. CLC Bio Genetics Workbench 3.0.0
- Processing SOLiD data with CLC bio Genomics work bench
- Sample prep for RNA-seq from low abundance RNA
- PubMed: Massive transcriptional start site analysis of human genes in hypoxia cells.
- How many amounts of mRNA do you start the pair end sequencing?
- snap frozen vs formaldehyde-fixed paraffin tissue samples
- SOLiD RNA-Seq protocol ver 2 - no PCR products
- ERANGE and other packages for RNAseq analysis
- browsing Cloonan et al RNA-seq data
- why low mapping rates for RNAseq?
- Error rate of 51 cycle mRNA Seq
- ERANGE: runRNAPairedAnalysis.sh with error at the rnafarPairs.py step
- TopHat questions
- GFF file for TopHat
- Expanded genome for A. thaliana to use with Erange?
- qPCR vs gene expression arrays vs short read RNA sequencing
- TopHat: no GFF3_file.expr in the output
- TopHat: output is not recognized by UCSC
- Build expanded genome for ERANGE
- Strand-preserving protocol for Illumina, 3'bias
- processing 454 rna-seq data
- How to analyze miRNA, antisense RNA, new regulon, etc. by RNA sequencing
- Where can I obtain GFF file for human?
- Population RNA-Seq
- Small RNA sequencing on Illumina
- Tag-Seq Data Analysis
- RNA-seq bias
- Best Technology for Digital Gene Expression
- Alternative to casava for variation analysis in RNA?
- low input for RNA preparation
- Tophat running error 1?
- wheat transcriptomes
- tophat -r mate inner distance
- Using tophat results via UCSC genome browser
- Intron retain detection using Solexa RNA-seq
- Next gen sequencing: urgent and updated instrument comparison
- uMACS cDNA kits for mRNA-seq sample prep
- Power calculations for expt design
- miR sequencing: miR and miR*, sense and antisense
- ERANGE: map to transcriptome
- DEGseq
- De-Novo transcriptome with 454 Titanium
- RNA-seq webinar
- Should identical reads be reduced to a single count?
- % matching problem- RNA_Seq
- the downstream analysis of RNA-seq
- deepBase: annotating and discovering small and long RNAs from deep sequencing data
- Comprehensive TopHat manual?
- Tophat/Cufflinks/RNASeq short-read aligners and pseudogenes
- Longer reads => more errors?
- RNA-seq cDNA preparation
- how to retrieve human rRNA annotation
- ERANGE problems!
- TopHat and the GFF3 file
- Anyone with Solexa RNA-seq 75+bp for non-model sps with no close reference genome?
- Tophat: report *only* novel splice junctions?
- Sequencing depth needed
- TopHat: ambiguous hits are only reported for one of the two paired end reads
- Alternative splicing detection using RNA-seq
- How to convert cufflinks output to raw counts
- threshold
- problem with Illumina PE RNA seq alingment
- Test datasets for judging RNA-seq alternative splicing detection tools
- RNA-seq reads mapping to coding regions
- How will trimming low-quality ends of Illumina reads affect TopHat and Cufflinks?
- Over represesented tags at 3'UTR - Illumina RNAseq
- Depth of coverage variation in RNA Seq
- problem in using ERANGE
- Bioanalyzer profile after ribominus treatment
- Theoretical problem for RNA-Seq Mapping
- RNAseq time course data
- Biorupting cDNA
- Tophat versus Maq
- SplitSeek - de novo detection of splice junctions
- RNA-Seq, software stats
- Anyone with Solexa RNA-seq 150+bp for non-model sps with no close reference genome?
- Quantifying trascript levels using RNA-seq
- separating indexed and nonindex sequences
- Detecting fusion transcripts in PE_RNA-Seq
- polyA+ yields from total RNA?
- ERANGE - getsplicefa.py
- Too many reads mapping towards intronic region
- RNA-Seq data set?
- SOAPals, for finding splice junctions
- Problem with Tophat and Cufflinks
- Tophat junctions.bed
- quality of RNA needed for prokaryotic RNA-seq?
- house-keeping genes in RNA-seq data sets?
- RNA-Seq biology
- software for RNA-seq data analysis
- Analysing RNA seq data
- extract assembled transcripts
- RNA-seq mapping
- tuning the tophat/cufflink pipeline
- about SRA paired datasets
- High wrong/miss loci rate by assembling transcripts
- RNA-seq output
- Ribosome associated mRNA
- problem running TopHat
- run cufflink, cuffcompare and cuffdiff workflow
- What mRNA-input for cDNA sequencing?
- agilent
- How much does the uniquely mapping matter?
- Spike sequence for ERANGE
- Best RNA-seq program for unpaired reads
- TopHat multireads?
- cufflinks memory allocation error.
- making miRNA libraries
- Getting specific Exon sequences from Transcriptome
- RNA-seq read distribution
- Testing Cufflinks
- Transcription Start Site Profiling from 10ng of total RNA
- HMMSplicer : new software for finding splice junctions in RNA-Seq data
- Kits for DGE on Illumina GA/HiSeq
- Ribosomal removal problem
- RNAi questions from a bioinformatician
- how much sequence is needed to cover a mouse transcriptome
- RNA cleanup after fragmentation - illumina
- Velvet/Oases transcript expression level?
- RNA-seq data sample
- ?'s about cuffdiff without genome, and about results
- Estimation of expression levels
- questions about RNA-Seq
- Error message in cuffcompare
- Tophat: some .sam files empty and some not
- RNA-seq file format of the near future
- question about cuffdiff
- Using RNASeq Data to Identify Differential RNA editing
- Costs
- EMBOSS and BFAST interference?
- Tophat's accepted_hits.sam reports all the ISIZEs equal zero
- What's your recommended RNA fragmentation method?
- RNA-seq, RPKM and heatmap???
- Tophat, Cufflinks and replicates
- Cufflinks, Cuffdiff and annotation
- Allelic imbalance and expression
- Cufflinks executables not working
- linear amplification of bacterial mRNA generates long molecules
- Tophat Error
- Problem with high background in some RNA-seq samples
- Supercript III SuperMix
- agilent small RNA chip says I have 55% miRNA!!??
- The T4 RNA Ligase in Small RNA Illumina Kit
- fragmented RNA and T4 PNK
- Has anyone used r-quant?
- RNA-Seq without reference
- Splice aware RNA-seq analysis
- de novo assembly of micrbiome samples
- Question about transcriptome
- Tophat command line options
- Computer spec for RNA-seq analysis.
- RNA-Seq to gene expression
- RNA-seq & gene annotation
- Cufflinks output - Next wat?
- Cufflinks SAM file sort problem
- ALEXA-Seq : Alternative expression analysis by RNA sequencing paper
- Differential analysis of non coding RNA seq
- Ribosomal RNA contamination assessment
- Myrna stops in paired bowtie alignment
- tophat strand info?
- Myrna stops in statistics stage
- Exon-Junction mapping: re-assigning CDS-mapped reads to chromosomes
- Regarding Unique reads, Unique alignments
- Myrna stops in Align stage
- Myrna new reference jar
- Size-selection in DSN normalisation
- bowtie parameter setting
- Isogroup Sequence
- DEG for paired samples, biological replicates
- Error with cuffdiff, version 0.9.0
- Combined mapping of RNA-Seq reads originating from multiple species
- When is Open reading frame=gene?
- Required sequencing depth for finding (nearly) all unique human transcripts
- Nonuniformity of reads across transcript length
- How to read modEncode RNA-seq data?
- Getting differentially expressed genes based on RPKM values
- Removing duplicate reads for tophat?
- Mapping and counting, small RNA seq. GA IIX
- Getting Gene-Level "Expression" Value
- How to BLAST a genome against Transcriptome sequence
- question about Solid data analysis using bowtie?
- Intron spikes in Nugen Ovation data?
- Sequencing RNA
- Single-end SOLiD data for TopHat
- Differential gene expression of gene clusters
- Annotation and RPKM measure after De Novo Assembly
- Multiple gene entries in cuffdiff output
- 5' cap and RNA-Seq
- RNA Seq alignment?
- Understanding tophat intermediate logs
- RNA-SEQ with no genome
- ribominus vs DSN
- Minimum number of reads mapping to a gene
- help with bowtie-inspect
- small RNA sequencing
- RNA-seq basecalls?
- ScriptSeq mRNA-Seq Library Preparation Kit
- data set from NCBI SRA
- Looking for Tophat GFF file (mm9)
- tophat with mixed paired end reads
- Small RNA sample prep images
- starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data
- Binary characters in cuffcompare result & Questions on cuffdiff
- Optimal read lenght for RNASeq
- How to analyze RNA-seq data ?
- fold change for genes with 0 reads
- True seq
- Expression check in mRNA-seq
- looking for solution to count the short reads in rice
- Tophat with colorspace
- denominator for normalization
- Questions about RNA fragmentation?
- qPCR validation of RNA-Seq data
- get the intergene region mapped rna-seq read
- Rfam
- Use of DSN normalization in SOLiD RNA-seq?
- cuffdiff for strand-unspecific sequencing
- RIP-Seq
- cDNA read map parameter
- error correction for RNA-seq reads
- Biological replicates for RNA-seq
- HiSeq versus Solid for DGE
- questions for cufflinks
- Tophat output BAM file ISIZE Error
- multiple FPKM problem for single gene in gene_exp.diff after running cuffdiff
- problems visualizing bam files in IGV
- Tophat not
- python in ABySS
- Free & Open Environment for RNA-seq analysis: Galaxy (http://usegalaxy.org)
- RSEQtools
- How to decide FPKM fo known genes
- RSEQtools
- multiple sample differential RNA editing/SNP after novoalignment
- Analysis of Directional mRNA-seq data / Illumina
- Error in coverting SRA to fastq
- tag density plots
- bacterial RNA-seq workbench options?
- Removing rRNA from RNA-Seq
- de novo transcriptome assembly
- Digital gene expression count from RNA-seq??
- Alignment at exon-exon junctions
- MAQ Map/Match Problem
- Optimal Analysis Software?
- TopHat -paired end vs single end reads
- transcript length bias in enrichment analysis and RPKM
- 2ndary structure prediction, mfe
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