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  1. Nimblegen arrays for targeted genome enrichment
  2. Getting Newbler
  3. 454 expected sequences and Tag for amplicon sequencing
  4. Nimblegen officially describes "SeqCap" genome decomplexing service
  5. New journal articles
  6. Help with 454 bar coded samples
  7. chromosome rearrangements
  8. High Short Reads %
  9. new 454 system
  10. 454 amplicon sequencing - gene family with large number of paralogs
  11. Starting the analysis of 454 data
  12. GS-FLX reagent shelf lives
  13. 454 Configuration Management
  14. Capture and 454
  15. Tech Summary: Roche's 454 GS20 / FLX / Titanium
  16. SNP calling on 454 data
  17. Mixed fragment size normalized cDNA sequencing
  18. Plasmid contamination in Long Tag Paired End library
  19. 454 Assembly viewer
  20. Deletion detection on seq-cap experiments
  21. Outlier in Newbler
  22. 454 homopolymer errors or????
  23. DNA Shearing for 454
  24. Titanium software (MPI mode)
  25. 454 Maintenace wash
  26. 454: Unmapped contigs after Reference Assembly
  27. Nimblegen Seq Capture Vs RainDance Technologies
  28. Depth viewer for 454 data.
  29. idle 454 ?
  30. gsAssembler / newbler hangs during (large?) assembly
  31. 454 Library / Emulsion / Instrument Protocols (October 2008)
  32. How to align contigs?
  33. question about coverage, .ace file.
  34. Roche's gsMapper
  35. How to explain this scenario ?
  36. 454 assemly
  37. launching gsAssembler in Fedora
  38. Homopolymer error in 454 sequencing data
  39. 454 sequencing data coverage
  40. newbler background
  41. sfffile converting quality values
  42. System requirements linux comp. for off-machine assembly/analysis
  43. compare GSMapper and BLAT
  44. Uniform droplet size?
  45. Recommendation from 454 for Titanium PE/Shotgun
  46. gsRunProcessor: error with v.2.0.00.22
  47. Roche Software - Slow GUI
  48. Is 10x coverage suitable for resequecing 1Gb genome using 454?
  49. Comparing SNP/indel detection tools on 454
  50. Tween Concentration in Maintenance Wash
  51. Poor enrichment...defective enrichment beads?
  52. Want to generate more data to fill in gaps
  53. Short reads in Titanium
  54. Alternative sequence enrichment methods
  55. Identifying collapsed repeats and other misassemblies
  56. Titanium kit - short reads
  57. Seqcap service
  58. GS FLX & Illumina
  59. 454 for RNA-Seq for 2 group comparison
  60. Duplicate reads ("same start" reads) in 454 FLX/Titanium shotgun runs
  61. cDNA synthesis kits with titanium
  62. 454 titanium sequence company
  63. 454 homopolymer error rate
  64. what's clipping point?
  65. getting reads not filtered?
  66. Poly(A) Tail treatment?
  67. postAnalysisScript.sh
  68. @454Sequencing on twitter!
  69. Roche soft Error: "At least one read sequence...."
  70. Turn off KeyPass Filter?
  71. Amplicon sequencing using Titanium technology
  72. Titanium problems
  73. Newbler --- classify many reads as Repeat
  74. Question --Incremental assembly using Nembler
  75. emPCR robot?
  76. Assessing a 454 run?
  77. 454 Vs Sanger
  78. gsMapper issues
  79. Control read variation
  80. GS Mapper output to consed shows dimmed ends with good sequence?
  81. Lims
  82. Titanium Runs
  83. small DNA sample library prep
  84. Summary Statistics in Newbler?
  85. advice for de novo assembly of plant genome using 454
  86. Titanium PE yields?
  87. emulsion droplets
  88. UTP and emPCR
  89. Titanium: Does it suck?
  90. Titanium upper and lower case bases
  91. GS FLX data analysis software manual
  92. Size Selection Tricks??
  93. Anyone know what the fill-in enzyme is?
  94. emPCR additive
  95. Roche software update 2.0.01.12
  96. Buying reagents from outside source to replace the 454 DNA library kit
  97. Different NextGen platforms sharing the same space
  98. primers and adaptors
  99. gsMapper to SAM/BAM
  100. gsassembler.
  101. amplicon size for titanium?
  102. gsMapper and compiling unmapped reads
  103. Number of Reads in 454 Library
  104. Finding Raw 454 Data
  105. Low Molecular Weight sample and primer dimers
  106. Replacement/generic Mock Amplification Mix
  107. suppression subtractive hybridization and 454
  108. Error Bar in 454's Flowgram
  109. Sequencing repeats: how to?
  110. 454 assembling against reference genome
  111. 454 runAssembly contig lengths
  112. miRNA in transcriptome or genome datasets?
  113. Software hangs on maintenance wash
  114. Renaming reads within SFF files
  115. 1/2 read and coverage?
  116. seqence on DNA capture bead of Titanium diff from FLX Standard?
  117. How quantitative is contig coverage?
  118. pyrotag process
  119. ReferenceMapper: Annotation files & known SNPs
  120. Difference between 454 pair end library and 454 standard library
  121. How to determine 454 paired end adaptor sequence
  122. what's the retro-fitted reaction in pyrosequencing
  123. 454 titanium emulsion PCR problems?
  124. OTF Ti signal processing
  125. Discussion and explanation about Roche's 454 GS20 / FLX / Titanium?!
  126. improper bead deposition
  127. Titanium - high fraction of short reads
  128. non paired adapters in 454 data
  129. MIRA:454 scaffolds polishing by Illumina reads discussion
  130. How to get started analysing 454 data
  131. gsAssembler v2.0.1 red X's in parameters
  132. REM e System for enrichment
  133. PCR Primer Design Software for Gap-closure
  134. Ti vs. FLX library construction
  135. Running assisted assemblies with runAssembly
  136. How are raw well numbers determined?
  137. emPCR additive
  138. Structural Variation with 454 Reads
  139. various SMART cDNA methods for transcriptome sequencing
  140. Enrichment with AGILENT's Sureselect target enrichment system
  141. Roche GS Junior mini 454 coming 2010
  142. WGS in one region, Amplicons in another
  143. Real biological 454 data publicly available for benchmarking
  144. emulsion pcr - one template-fragment per bead?
  145. 3-5% more seq from new Roche software
  146. read length of GS FLX Titanium
  147. New 454 emulsion creation
  148. Roche 454 Paired End with Covaris Shearing
  149. sff 454 files into fasta
  150. Raw wells?
  151. Amplicon library titration
  152. N25 & N75 sequence index
  153. Does splitting run reduce read number?
  154. Control DNA fragments sequences on titanium
  155. Using multiple MIDs in titanium sequence runs
  156. newbler cpu core usage
  157. PyroNoise on Mac OS X?
  158. Performing Hybrid Assemblies With Newbler
  159. trimming issue
  160. Newbler assembly - excluding specific reads?
  161. gsMapper contigs
  162. Rubber gasket vs. Molecular Markers
  163. Rapid Libraries
  164. Paired-end & shotgun reads
  165. mira3 output
  166. Removing primers
  167. mira parameters for SNP search in transcriptome de novo
  168. real world 454 sequencing data analysis examples?!
  169. Extracting contig info and singletons
  170. Amplicon and other library types in the same run?
  171. Homopolymer run errors, polyA bias
  172. Paper: Fully automated process for barcoded libraries for 454
  173. Target Sequence Enrichment 454
  174. Error using sff_extract.
  175. Flowgram signals to quality score
  176. coverage for amplicon seq?
  177. 454 Consumable Deliveries
  178. 454 quality score, z-score,..
  179. rearreangment points
  180. GS FLX Titanium series and small fragment
  181. 454assembly using Newbler: job time expectation?
  182. sequencing gene more than 10kb
  183. New England Biolabs Reagents
  184. coverage
  185. Newbler 2.3 on Ubuntu- Anyone?
  186. rapid cDNA library normalization?
  187. Roche Gs* software
  188. Question about evaluation of 454 sequence
  189. Calculation of Homopolymer errors
  190. standard operating procedure 454 analysis
  191. Detection of alternative splicing events from 454 output
  192. primer seq for assembly?
  193. Titanium Amplicon run.
  194. RAPID Libraries adaptor+key sequences
  195. best primers for 16S amplicon sequencing
  196. 454 Detection Probability
  197. Sequencing of E. coli strains
  198. Rapid Library Kit contents
  199. 454 Roche Titanium Run Costs
  200. Targeted sequencing
  201. Filtering clonal reads
  202. 454 supply issues?
  203. Newbler's algorithm -> overlap or de Brujin graph?
  204. standard chemistry
  205. 454 and cluster operating systems - patching Fedora
  206. problems about 454 transcription data analysis
  207. 16 lane run leakage
  208. What to do with leading T's and G's?
  209. Contigs from gsAssembler / newbler
  210. Singletons -Amplicon sequencing
  211. Using sff tools to Extract Read Subsets
  212. Problems cDNA sequencng
  213. Bead preparation for "GS Junior" with ABI EZ Bead Dystem
  214. sffinfo -s inputfile
  215. something about my 454 result
  216. Genome Sequencer Data Analysis software & CygWin
  217. Alternatives to sfffile & sffinfo
  218. Nested PCR amplicons
  219. Fluidigm Access Array
  220. CPB correction with emPCR format change
  221. Overcalled A's in my 454 data
  222. PyroNoise -DAT files
  223. FLX vs Titanium, Lib-L vs Lib-A, Amplicon Libraries = confusion
  224. Pool amplicons on a plate
  225. low cDNA concentration after the RAPID protocol
  226. running amplicons together with non amplicon lanes
  227. runAssembly error
  228. Memory Usage in Newbler 2.3
  229. fasta+qual = sff??
  230. LMW band in paired end libraries?
  231. SFF Read names
  232. problem with the ligation of adaptator- Rapid library
  233. Completely new to this and out of my depth
  234. Quantitative pyrosequencing?
  235. Rapid library prep and Nimblegen enrichment
  236. "rapid" vs "general" MID adapters
  237. library: control signal ratio
  238. gsMapper problem
  239. GS Junior - bead issues.
  240. Estimating genome size and coverage
  241. 454 assembly of repetitive region
  242. Access Array (platform from Fluidigm) for 454 library preparation
  243. Going from biotinylated primer to unlabeled primer in emPCR
  244. 454 software installation
  245. Quantification and between run replication
  246. calculating expected reads
  247. SureSelect and Rapid MID Libraries
  248. 454 Titanium error rate ?
  249. Delivery problem for emPCR kits
  250. HPLC purification of 454 fusion primers