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  1. RNA-seq with paired-end reads
  2. Erange
  3. mRNA preparation for RNA-Seq
  4. Why are the ends different in RNA seq?
  5. Abi Solid WT Sample Data vs. CLC Bio Genetics Workbench 3.0.0
  6. Processing SOLiD data with CLC bio Genomics work bench
  7. Sample prep for RNA-seq from low abundance RNA
  8. PubMed: Massive transcriptional start site analysis of human genes in hypoxia cells.
  9. How many amounts of mRNA do you start the pair end sequencing?
  10. snap frozen vs formaldehyde-fixed paraffin tissue samples
  11. SOLiD RNA-Seq protocol ver 2 - no PCR products
  12. ERANGE and other packages for RNAseq analysis
  13. browsing Cloonan et al RNA-seq data
  14. why low mapping rates for RNAseq?
  15. Error rate of 51 cycle mRNA Seq
  16. ERANGE: runRNAPairedAnalysis.sh with error at the rnafarPairs.py step
  17. TopHat questions
  18. GFF file for TopHat
  19. Expanded genome for A. thaliana to use with Erange?
  20. qPCR vs gene expression arrays vs short read RNA sequencing
  21. TopHat: no GFF3_file.expr in the output
  22. TopHat: output is not recognized by UCSC
  23. Build expanded genome for ERANGE
  24. Strand-preserving protocol for Illumina, 3'bias
  25. processing 454 rna-seq data
  26. How to analyze miRNA, antisense RNA, new regulon, etc. by RNA sequencing
  27. Where can I obtain GFF file for human?
  28. Population RNA-Seq
  29. Small RNA sequencing on Illumina
  30. Tag-Seq Data Analysis
  31. RNA-seq bias
  32. Best Technology for Digital Gene Expression
  33. Alternative to casava for variation analysis in RNA?
  34. low input for RNA preparation
  35. Tophat running error 1?
  36. wheat transcriptomes
  37. tophat -r mate inner distance
  38. Using tophat results via UCSC genome browser
  39. Intron retain detection using Solexa RNA-seq
  40. Next gen sequencing: urgent and updated instrument comparison
  41. uMACS cDNA kits for mRNA-seq sample prep
  42. Power calculations for expt design
  43. miR sequencing: miR and miR*, sense and antisense
  44. ERANGE: map to transcriptome
  45. DEGseq
  46. De-Novo transcriptome with 454 Titanium
  47. RNA-seq webinar
  48. Should identical reads be reduced to a single count?
  49. % matching problem- RNA_Seq
  50. the downstream analysis of RNA-seq
  51. deepBase: annotating and discovering small and long RNAs from deep sequencing data
  52. Comprehensive TopHat manual?
  53. Tophat/Cufflinks/RNASeq short-read aligners and pseudogenes
  54. Longer reads => more errors?
  55. RNA-seq cDNA preparation
  56. how to retrieve human rRNA annotation
  57. ERANGE problems!
  58. TopHat and the GFF3 file
  59. Anyone with Solexa RNA-seq 75+bp for non-model sps with no close reference genome?
  60. Tophat: report *only* novel splice junctions?
  61. Sequencing depth needed
  62. TopHat: ambiguous hits are only reported for one of the two paired end reads
  63. Alternative splicing detection using RNA-seq
  64. How to convert cufflinks output to raw counts
  65. threshold
  66. problem with Illumina PE RNA seq alingment
  67. Test datasets for judging RNA-seq alternative splicing detection tools
  68. RNA-seq reads mapping to coding regions
  69. How will trimming low-quality ends of Illumina reads affect TopHat and Cufflinks?
  70. Over represesented tags at 3'UTR - Illumina RNAseq
  71. Depth of coverage variation in RNA Seq
  72. problem in using ERANGE
  73. Bioanalyzer profile after ribominus treatment
  74. Theoretical problem for RNA-Seq Mapping
  75. RNAseq time course data
  76. Biorupting cDNA
  77. Tophat versus Maq
  78. SplitSeek - de novo detection of splice junctions
  79. RNA-Seq, software stats
  80. Anyone with Solexa RNA-seq 150+bp for non-model sps with no close reference genome?
  81. Quantifying trascript levels using RNA-seq
  82. separating indexed and nonindex sequences
  83. Detecting fusion transcripts in PE_RNA-Seq
  84. polyA+ yields from total RNA?
  85. ERANGE - getsplicefa.py
  86. Too many reads mapping towards intronic region
  87. RNA-Seq data set?
  88. SOAPals, for finding splice junctions
  89. Problem with Tophat and Cufflinks
  90. Tophat junctions.bed
  91. quality of RNA needed for prokaryotic RNA-seq?
  92. house-keeping genes in RNA-seq data sets?
  93. RNA-Seq biology
  94. software for RNA-seq data analysis
  95. Analysing RNA seq data
  96. extract assembled transcripts
  97. RNA-seq mapping
  98. tuning the tophat/cufflink pipeline
  99. about SRA paired datasets
  100. High wrong/miss loci rate by assembling transcripts
  101. RNA-seq output
  102. Ribosome associated mRNA
  103. problem running TopHat
  104. run cufflink, cuffcompare and cuffdiff workflow
  105. What mRNA-input for cDNA sequencing?
  106. agilent
  107. How much does the uniquely mapping matter?
  108. Spike sequence for ERANGE
  109. Best RNA-seq program for unpaired reads
  110. TopHat multireads?
  111. cufflinks memory allocation error.
  112. making miRNA libraries
  113. Getting specific Exon sequences from Transcriptome
  114. RNA-seq read distribution
  115. Testing Cufflinks
  116. Transcription Start Site Profiling from 10ng of total RNA
  117. HMMSplicer : new software for finding splice junctions in RNA-Seq data
  118. Kits for DGE on Illumina GA/HiSeq
  119. Ribosomal removal problem
  120. RNAi questions from a bioinformatician
  121. how much sequence is needed to cover a mouse transcriptome
  122. RNA cleanup after fragmentation - illumina
  123. Velvet/Oases transcript expression level?
  124. RNA-seq data sample
  125. ?'s about cuffdiff without genome, and about results
  126. Estimation of expression levels
  127. questions about RNA-Seq
  128. Error message in cuffcompare
  129. Tophat: some .sam files empty and some not
  130. RNA-seq file format of the near future
  131. question about cuffdiff
  132. Using RNASeq Data to Identify Differential RNA editing
  133. Costs
  134. EMBOSS and BFAST interference?
  135. Tophat's accepted_hits.sam reports all the ISIZEs equal zero
  136. What's your recommended RNA fragmentation method?
  137. RNA-seq, RPKM and heatmap???
  138. Tophat, Cufflinks and replicates
  139. Cufflinks, Cuffdiff and annotation
  140. Allelic imbalance and expression
  141. Cufflinks executables not working
  142. linear amplification of bacterial mRNA generates long molecules
  143. Tophat Error
  144. Problem with high background in some RNA-seq samples
  145. Supercript III SuperMix
  146. agilent small RNA chip says I have 55% miRNA!!??
  147. The T4 RNA Ligase in Small RNA Illumina Kit
  148. fragmented RNA and T4 PNK
  149. Has anyone used r-quant?
  150. RNA-Seq without reference
  151. Splice aware RNA-seq analysis
  152. de novo assembly of micrbiome samples
  153. Question about transcriptome
  154. Tophat command line options
  155. Computer spec for RNA-seq analysis.
  156. RNA-Seq to gene expression
  157. RNA-seq & gene annotation
  158. Cufflinks output - Next wat?
  159. Cufflinks SAM file sort problem
  160. ALEXA-Seq : Alternative expression analysis by RNA sequencing paper
  161. Differential analysis of non coding RNA seq
  162. Ribosomal RNA contamination assessment
  163. Myrna stops in paired bowtie alignment
  164. tophat strand info?
  165. Myrna stops in statistics stage
  166. Exon-Junction mapping: re-assigning CDS-mapped reads to chromosomes
  167. Regarding Unique reads, Unique alignments
  168. Myrna stops in Align stage
  169. Myrna new reference jar
  170. Size-selection in DSN normalisation
  171. bowtie parameter setting
  172. Isogroup Sequence
  173. DEG for paired samples, biological replicates
  174. Error with cuffdiff, version 0.9.0
  175. Combined mapping of RNA-Seq reads originating from multiple species
  176. When is Open reading frame=gene?
  177. Required sequencing depth for finding (nearly) all unique human transcripts
  178. Nonuniformity of reads across transcript length
  179. How to read modEncode RNA-seq data?
  180. Getting differentially expressed genes based on RPKM values
  181. Removing duplicate reads for tophat?
  182. Mapping and counting, small RNA seq. GA IIX
  183. Getting Gene-Level "Expression" Value
  184. How to BLAST a genome against Transcriptome sequence
  185. question about Solid data analysis using bowtie?
  186. Intron spikes in Nugen Ovation data?
  187. Sequencing RNA
  188. Single-end SOLiD data for TopHat
  189. Differential gene expression of gene clusters
  190. Annotation and RPKM measure after De Novo Assembly
  191. Multiple gene entries in cuffdiff output
  192. 5' cap and RNA-Seq
  193. RNA Seq alignment?
  194. Understanding tophat intermediate logs
  195. RNA-SEQ with no genome
  196. ribominus vs DSN
  197. Minimum number of reads mapping to a gene
  198. help with bowtie-inspect
  199. small RNA sequencing
  200. RNA-seq basecalls?
  201. ScriptSeq mRNA-Seq Library Preparation Kit
  202. data set from NCBI SRA
  203. Looking for Tophat GFF file (mm9)
  204. tophat with mixed paired end reads
  205. Small RNA sample prep images
  206. starBase: deciphering miRNA-target interactions from CLIP-Seq and Degradome-Seq data
  207. Binary characters in cuffcompare result & Questions on cuffdiff
  208. Optimal read lenght for RNASeq
  209. How to analyze RNA-seq data ?
  210. fold change for genes with 0 reads
  211. True seq
  212. Expression check in mRNA-seq
  213. looking for solution to count the short reads in rice
  214. Tophat with colorspace
  215. denominator for normalization
  216. Questions about RNA fragmentation?
  217. qPCR validation of RNA-Seq data
  218. get the intergene region mapped rna-seq read
  219. Rfam
  220. Use of DSN normalization in SOLiD RNA-seq?
  221. cuffdiff for strand-unspecific sequencing
  222. RIP-Seq
  223. cDNA read map parameter
  224. error correction for RNA-seq reads
  225. Biological replicates for RNA-seq
  226. HiSeq versus Solid for DGE
  227. questions for cufflinks
  228. Tophat output BAM file ISIZE Error
  229. multiple FPKM problem for single gene in gene_exp.diff after running cuffdiff
  230. problems visualizing bam files in IGV
  231. Tophat not
  232. python in ABySS
  233. Free & Open Environment for RNA-seq analysis: Galaxy (http://usegalaxy.org)
  234. RSEQtools
  235. How to decide FPKM fo known genes
  236. RSEQtools
  237. multiple sample differential RNA editing/SNP after novoalignment
  238. Analysis of Directional mRNA-seq data / Illumina
  239. Error in coverting SRA to fastq
  240. tag density plots
  241. bacterial RNA-seq workbench options?
  242. Removing rRNA from RNA-Seq
  243. de novo transcriptome assembly
  244. Digital gene expression count from RNA-seq??
  245. Alignment at exon-exon junctions
  246. MAQ Map/Match Problem
  247. Optimal Analysis Software?
  248. TopHat -paired end vs single end reads
  249. transcript length bias in enrichment analysis and RPKM
  250. 2ndary structure prediction, mfe