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  1. Epigenomics - ChIP-Seq, BS-Seq, etc.
  2. Chip-seq sample prep protocols for 454?
  3. ChIP seq sample prep for Illumina
  4. some questions about ChIP-Seq replicates/controls
  5. ChIP-seq problem
  6. A brief review of recent ChIP-Seq tools literature
  7. Regions of extreme bias in histone modification runs
  8. unique mapping for chip-seq?
  9. PubMed: Genome-wide histone methylation profile for heart failure.
  10. Epi Review: "Epigenetics meets next-generation sequencing" (OPEN ACCESS!)
  11. New software: PeakSeq enables systematic scoring of ChIP-seq expts
  12. CpG Islands vs CHIP-Seq data
  13. Amount of ChIP DNA required for Solexa seqeuncing
  14. PubMed: ChIP-seq accurately predicts tissue-specific activity of enhancers.
  15. No enrichment in ChIP-seq
  16. The Sixth Base: 5-hydroxymethylcytosine enriched in mammalian brains
  17. MedIP-Seq and Batman
  18. ChIP seq-% alignment
  19. Mapping Bisulphite converted sequence
  20. BSMAP: whole genome Bisulfite Sequence MAPping program
  21. watch out, biases!
  22. ChIP-seq of possibly high repeated sequences
  23. How to compute IP efficiency
  24. Methylation patterns through Methyl-Seq
  25. Human DNA methylomes at base resolution show widespread epigenomic differences
  26. MeDIP-Seq (Illumina/Solexa)
  27. a question about "regions"
  28. Long peak length from ChIP-seq data
  29. Chip-Seq: best value/money read length SE/PE ?
  30. Help with bisulfite sequencing
  31. searching tool for ChIP-seq analysis of histone modification analysis
  32. chip seq and TRANSFAC
  33. Shearing DNA for Chip-seq
  34. ChIP-Seq and Bisulfite sequencing coverage
  35. ChIP-Seq comparisons
  36. ChIP-seq data analysis for beginner
  37. Covaris vs. Biorupter
  38. Strange higher size amplicon in ChIP seq Library!!
  39. Peaks at every promoter with Input material
  40. Epigenetics Phone Survey--$50 Gift Card
  41. Statistical comparison of more than two ChIP-seq experiments
  42. Can Chromasig be used to analyse multiple DNA methylation samples?
  43. where can i found chip-seq data of Drosophila
  44. Question: Is there another new methylated DNA base out there?
  45. Optimum input DNA sequencing depth
  46. Negative control sequencing
  47. Chip-seq analyse using USeq
  48. WGA Amplification for ChIP samples prior to Seq?
  49. a kit for hydroxymethylcytosine analysis
  50. From Affy probe sets/gene symbols to genomic coordinates?
  51. NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA m
  52. Specificty of Histone mod Abs and controls
  53. ChIP Seq data analysis
  54. Chip-seq protocols and chromatin prep
  55. ChIP and SDS
  56. Calling peaks from NRSF ChIP-Seq with USeq
  57. Which BS-seq analysis tool to choose?
  58. Genome wide methylation dataset
  59. Understanding the qmap bis-seq format
  60. Non-specific binding of control antibodies for ChIP-seq
  61. negative control or not
  62. Rrbs
  63. Protein G magnetic beads and ChIP-seq
  64. which is better, paired or single end
  65. CisGenome Analysis
  66. Some queries on DNA methylation when processing the BS-seq data
  67. Epigenome reference: BI submissions to SRA
  68. Best protein tag for ChIP
  69. ChIPseq for histone modifications
  70. significant peaks in WIG format
  71. combinatorial histone methylation patterns
  72. Chromatin micrococcal digestion
  73. RRBS library prep.
  74. which one indicate strand on bowtie outputs?
  75. ChIP-seq with very small amount of tissue
  76. Experience with ChIA-PET?
  77. CpG island detection
  78. technical replicates uncorrelate with each other
  79. ChIP- Different DNA size for Input DNA and ChIP DNA on Agilent Bioanalyzer
  80. 10 Mb signal-free region in mouse chromosomes
  81. ChIPseq on tissue - eliminating background
  82. Fasta with one entry per chromosome (for methylation analysis and others)
  83. Methylation Analysis
  84. ChIP-seq on Drosophila embryos using Illumina
  85. Bisulphite sequencing on Illumina Paired End 100bp reads
  86. expectations of high quality chip seq experiments
  87. how do you normalize MBD sequencing data?
  88. Two previously unknown modified cytosine bases found...
  89. BS-Seq from a single cell?
  90. TruSeq - ChIP-seq library construction
  91. ChIP-Seq with HA-tagged protein
  92. More information on RIP-seq
  93. Very high duplication of sequences in ChIP-Seq sequencing results
  94. how to compare peak signals from two independent samples
  95. MEDIP in invertebrates
  96. Beginner
  97. Comparing input peaks to IP peaks
  98. WGA in MeDip-Seq
  99. Merging MACS Peak analysis +/- duplicates?
  100. Using MACS for histone marks with GLOBAL lambda
  101. ChIP-Seq using 100bp paired-end reads
  102. Minimum Criteria to Publish ChIP-seq data
  103. Starting concentration of sample/control in ChIP Seq
  104. MeDIP-seq - input sample needed?
  105. ChIP - shearing with the Covaris S2
  106. MBD-Seq Help
  107. Peaks Analysis
  108. Indexing ChIPseq libraries using Illumina's TruSeq and ChIPseq kits
  109. Bismark paired-end positions
  110. Bisulphite Sequencing Proof-reading or NOT proof-reading?
  111. Statistical comparison of chip-seq for 2 conditions
  112. Good anti-GFP/YFP for ChIP-Seq?
  113. Epigenomics Workshop at ABRF 2012 Meeting
  114. Standards, Guidelines and Best Practices for ChIP-seq
  115. Bisulfite sequencing - filtering by min. conversion rate
  116. BS-Seq mapping efficiency, what can be expected?
  117. MBD-seq (or any enrichment-seq) read number <-> biology?
  118. New Epigenetics Research Video and Upcoming Webinar
  119. Bismark paired-end read orientation
  120. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
  121. visualisation of chip-seq profiles ... seqminer?
  122. Methylation calling tools, what works well?
  123. CHIP Seq
  124. BS-Seq on Repetitive Region
  125. TSS plot. Drop of the signal at TSS.
  126. Epigenetics resources page featuring exclusive interviews & conference presentations
  127. Illumina BS-seq library prep query
  128. Upcoming Epigenetics Virtual Poster Presentation
  129. Downsampling a BAM file
  130. refseq in BSP output file using BSMAP
  131. Small fragments post IP
  132. Unusually high yield with ChIP?
  133. my problem with agilent Sureselect methy-seq kit
  134. Problems with Medip-chip data analysis using batman
  135. Sticky crosslinked cells
  136. SICER: redundancy threshold parameter
  137. Mapping ChIP-Seq data which is in a excel sheet
  138. bicycle: bisulfite-based methylcytosine caller
  139. genome bisulfite sequencing
  140. Gene Sums for Chip-Seq Data
  141. BSSeq on whole genome - BS befor library prep?
  142. Chip-Seq and Gene expression data
  143. meDIP-chip/meDIP-seq/MethylCap-seq using mouse DNA
  144. swDMR: a sliding window approach to identify DMR based on bisulfite sequencing
  145. Concern about short fragment size and high duplication rate in paired-end ChIP-Seq
  146. BSSim: Bisulfite sequencing simulator for next-generation sequencing.
  147. Non-BS mismatch count in .SAM (esp. Bismark)?
  148. piRNAs sequence files in fasta format for rat and mapping small RNA seq reads
  149. How to deal with .wig files!! P
  150. ChIP-seq data analysis specifically for histone modifications
  151. Simple question: Who actually discovered 5 methyl C?
  152. Chip-seq price?
  153. ChIP-seq fastq.gz files
  154. Sonication's fault or gel's fault?
  155. Genomic DNA shearing with Covaris E220
  156. ChIP reagents
  157. Why there are blobs in my sheared DNA bands?
  158. Join Us for 2 Upcoming Epigenetics eSeminars
  159. All Human Non Coding RNA Foldings - Youtube Video
  160. Is my chip-seq data garbage?
  161. Epigenetic pathway analysis?
  162. Method to detect DMR
  163. Filter for mapping quality or for properly paired reads??
  164. Question about sam output of Bismark
  165. Methyl-Seq Questions
  166. Question:Most convenient way to get annotation information for a chromosome location?
  167. Optimal Setup for MethylMiner-seq (ChIP-seq)
  168. Comprehensive List of transcription factor binding site databases based on ChIP-Seq
  169. Input required?
  170. Insert size for overlapped reads?
  171. How many inputs for each replicate/cell line
  172. Will over-amplification during library preparation "drown out" ChIPseq peaks?
  173. Public Mouse Methyl-seq Data?
  174. Is it ok to ChIP-Seq two samples when the ChIP worked better in one?
  175. methylation and genomics variation
  176. ChIPseq Library Prep Amplification: How many PCR cycles do you use?
  177. High PCR duplicate with library - possible cause?
  178. MedIp-seq Input data
  179. Is methylation data gathered from bisulfite sequencing noisy between biological reps?
  180. Annotate a bed file from Sureselect Kit(Methylseq)
  181. MeDIP-seq and compatible DNA adapters for multiplexing?
  182. Fastqc on Chip-Seq library: confusion
  183. Searching tool to convert MACS output (chr + coordinates) into genomic feature
  184. When to integrate the negative control?
  185. Tools to perform QC of methylation calling
  186. Is Separose bead protein G sufficient for ChIP-seq analyse?
  187. How to quantify reads at a location?
  188. How to build reference genome for targeted region(from a BED file) for alignment?
  189. Wierd SAM format chromosome column
  190. MeDIP-sequencing data amount required
  191. Medip sequencing services
  192. Can I analyze old blood samples?
  193. How to deal with biological replicates of nucleosome MNase-seq data?
  194. Audio Files Transcription
  195. D. Melanogaster ChIP
  196. Nice p-value, bad FDR
  197. For ChIP-seq, maximal coverage at a peak?
  198. Post-ChIP Sonication Protocol
  199. MeRIPseq and m6A-seq data processing
  200. transcription factor binding sites enrichment analysis
  201. MspI digestion - how is it supposed to look?
  202. Self designed Methylated Adapters
  203. which kit to use for whole genome BS-seq library?
  204. No DNA in ChIP IgG Control - Strange?
  205. Memory issues running Bismark/Bowtie alignment on a cluster
  206. ChIP-seq Analysis treated vs. non-treated vs. input controls?
  207. Directional vs. non-directional sequencing libraries
  208. CexoR: peak-pair calling in ChIP-exo data with replicates
  209. DNaseR - DNase-seq digita genomic footprinting in R
  210. How does MEME-ChIP selects the training set?
  211. How to do unique mapping in bowtie2
  212. Methylation Study
  213. Question about inputs for ChIP-seq
  214. BSmooth alignment problem
  215. MiSeq & Bisulphite Sequencing
  216. Colorspace bis-seq data analysis on Solid
  217. bsmooth aligner
  218. read alignment trimming
  219. Anyone has experience with .ylf (young lab format) files ?
  220. Target Enrichment from Bisulfite-treated DNA
  221. Bismark: paired-end low mapping efficiency
  222. Strange bisulfite libraries
  223. ChIP-seq library complexity
  224. Anyone using Bioruptor Pico?
  225. Unmapped reads (ChIP vs Input)
  226. statistical analysis of 454 bisulfite sequence data - small sample size
  227. The highest temperature tolerated by cross-linked chromatin
  228. Can ChIP Sequencing be used to make exploratory findings about histone methylation?
  229. MBD qPCR - shift in melt curve
  230. RRDS adapter mismatch design
  231. Hands-On Training in DNA Methylation Analysis
  232. Dangers of Over-amplifying ChIP-Seq Libraries
  233. Normalization with champ.norm in ChAMP Pakcage
  234. Problem of methylKit: Too many false positive?
  235. which kit for RRBS?
  236. DNase seq
  237. Chip seq transcription factor low DNA yield
  238. ChIP-seq
  239. Help for bisulphite primer design
  240. ChIPSeq after FACS
  241. MACS when sonication fragment size is a range of 300 to 700 bp
  242. Mapping Chip-seq with BWA or Bowtie2?
  243. Illumina sequencing for multiplexed RRBS
  244. whole genome bisulfite sequencing in mouse: how many reads required
  245. ssDNA library prep for meDIP
  246. Reply from NEB re: ssDNA library prep
  247. Dynabeads with diagenode magnets?
  248. ChIPSeq lilbrary prep for Miseq: NEB or TruSeq ?
  249. Methylation in the + strand influence the expression of gene in the - strand?
  250. Problems amplifying Ox-BS & BS template from TrueMethyl