- Epigenomics - ChIP-Seq, BS-Seq, etc.
- Chip-seq sample prep protocols for 454?
- ChIP seq sample prep for Illumina
- some questions about ChIP-Seq replicates/controls
- ChIP-seq problem
- A brief review of recent ChIP-Seq tools literature
- Regions of extreme bias in histone modification runs
- unique mapping for chip-seq?
- PubMed: Genome-wide histone methylation profile for heart failure.
- Epi Review: "Epigenetics meets next-generation sequencing" (OPEN ACCESS!)
- New software: PeakSeq enables systematic scoring of ChIP-seq expts
- CpG Islands vs CHIP-Seq data
- Amount of ChIP DNA required for Solexa seqeuncing
- PubMed: ChIP-seq accurately predicts tissue-specific activity of enhancers.
- No enrichment in ChIP-seq
- The Sixth Base: 5-hydroxymethylcytosine enriched in mammalian brains
- MedIP-Seq and Batman
- ChIP seq-% alignment
- Mapping Bisulphite converted sequence
- BSMAP: whole genome Bisulfite Sequence MAPping program
- watch out, biases!
- ChIP-seq of possibly high repeated sequences
- How to compute IP efficiency
- Methylation patterns through Methyl-Seq
- Human DNA methylomes at base resolution show widespread epigenomic differences
- MeDIP-Seq (Illumina/Solexa)
- a question about "regions"
- Long peak length from ChIP-seq data
- Chip-Seq: best value/money read length SE/PE ?
- Help with bisulfite sequencing
- searching tool for ChIP-seq analysis of histone modification analysis
- chip seq and TRANSFAC
- Shearing DNA for Chip-seq
- ChIP-Seq and Bisulfite sequencing coverage
- ChIP-Seq comparisons
- ChIP-seq data analysis for beginner
- Covaris vs. Biorupter
- Strange higher size amplicon in ChIP seq Library!!
- Peaks at every promoter with Input material
- Epigenetics Phone Survey--$50 Gift Card
- Statistical comparison of more than two ChIP-seq experiments
- Can Chromasig be used to analyse multiple DNA methylation samples?
- where can i found chip-seq data of Drosophila
- Question: Is there another new methylated DNA base out there?
- Optimum input DNA sequencing depth
- Negative control sequencing
- Chip-seq analyse using USeq
- WGA Amplification for ChIP samples prior to Seq?
- a kit for hydroxymethylcytosine analysis
- From Affy probe sets/gene symbols to genomic coordinates?
- NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA m
- Specificty of Histone mod Abs and controls
- ChIP Seq data analysis
- Chip-seq protocols and chromatin prep
- ChIP and SDS
- Calling peaks from NRSF ChIP-Seq with USeq
- Which BS-seq analysis tool to choose?
- Genome wide methylation dataset
- Understanding the qmap bis-seq format
- Non-specific binding of control antibodies for ChIP-seq
- negative control or not
- Rrbs
- Protein G magnetic beads and ChIP-seq
- which is better, paired or single end
- CisGenome Analysis
- Some queries on DNA methylation when processing the BS-seq data
- Epigenome reference: BI submissions to SRA
- Best protein tag for ChIP
- ChIPseq for histone modifications
- significant peaks in WIG format
- combinatorial histone methylation patterns
- Chromatin micrococcal digestion
- RRBS library prep.
- which one indicate strand on bowtie outputs?
- ChIP-seq with very small amount of tissue
- Experience with ChIA-PET?
- CpG island detection
- technical replicates uncorrelate with each other
- ChIP- Different DNA size for Input DNA and ChIP DNA on Agilent Bioanalyzer
- 10 Mb signal-free region in mouse chromosomes
- ChIPseq on tissue - eliminating background
- Fasta with one entry per chromosome (for methylation analysis and others)
- Methylation Analysis
- ChIP-seq on Drosophila embryos using Illumina
- Bisulphite sequencing on Illumina Paired End 100bp reads
- expectations of high quality chip seq experiments
- how do you normalize MBD sequencing data?
- Two previously unknown modified cytosine bases found...
- BS-Seq from a single cell?
- TruSeq - ChIP-seq library construction
- ChIP-Seq with HA-tagged protein
- More information on RIP-seq
- Very high duplication of sequences in ChIP-Seq sequencing results
- how to compare peak signals from two independent samples
- MEDIP in invertebrates
- Beginner
- Comparing input peaks to IP peaks
- WGA in MeDip-Seq
- Merging MACS Peak analysis +/- duplicates?
- Using MACS for histone marks with GLOBAL lambda
- ChIP-Seq using 100bp paired-end reads
- Minimum Criteria to Publish ChIP-seq data
- Starting concentration of sample/control in ChIP Seq
- MeDIP-seq - input sample needed?
- ChIP - shearing with the Covaris S2
- MBD-Seq Help
- Peaks Analysis
- Indexing ChIPseq libraries using Illumina's TruSeq and ChIPseq kits
- Bismark paired-end positions
- Bisulphite Sequencing Proof-reading or NOT proof-reading?
- Statistical comparison of chip-seq for 2 conditions
- Good anti-GFP/YFP for ChIP-Seq?
- Epigenomics Workshop at ABRF 2012 Meeting
- Standards, Guidelines and Best Practices for ChIP-seq
- Bisulfite sequencing - filtering by min. conversion rate
- BS-Seq mapping efficiency, what can be expected?
- MBD-seq (or any enrichment-seq) read number <-> biology?
- New Epigenetics Research Video and Upcoming Webinar
- Bismark paired-end read orientation
- MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
- visualisation of chip-seq profiles ... seqminer?
- Methylation calling tools, what works well?
- CHIP Seq
- BS-Seq on Repetitive Region
- TSS plot. Drop of the signal at TSS.
- Epigenetics resources page featuring exclusive interviews & conference presentations
- Illumina BS-seq library prep query
- Upcoming Epigenetics Virtual Poster Presentation
- Downsampling a BAM file
- refseq in BSP output file using BSMAP
- Small fragments post IP
- Unusually high yield with ChIP?
- my problem with agilent Sureselect methy-seq kit
- Problems with Medip-chip data analysis using batman
- Sticky crosslinked cells
- SICER: redundancy threshold parameter
- Mapping ChIP-Seq data which is in a excel sheet
- bicycle: bisulfite-based methylcytosine caller
- genome bisulfite sequencing
- Gene Sums for Chip-Seq Data
- BSSeq on whole genome - BS befor library prep?
- Chip-Seq and Gene expression data
- meDIP-chip/meDIP-seq/MethylCap-seq using mouse DNA
- swDMR: a sliding window approach to identify DMR based on bisulfite sequencing
- Concern about short fragment size and high duplication rate in paired-end ChIP-Seq
- BSSim: Bisulfite sequencing simulator for next-generation sequencing.
- Non-BS mismatch count in .SAM (esp. Bismark)?
- piRNAs sequence files in fasta format for rat and mapping small RNA seq reads
- How to deal with .wig files!! P
- ChIP-seq data analysis specifically for histone modifications
- Simple question: Who actually discovered 5 methyl C?
- Chip-seq price?
- ChIP-seq fastq.gz files
- Sonication's fault or gel's fault?
- Genomic DNA shearing with Covaris E220
- ChIP reagents
- Why there are blobs in my sheared DNA bands?
- Join Us for 2 Upcoming Epigenetics eSeminars
- All Human Non Coding RNA Foldings - Youtube Video
- Is my chip-seq data garbage?
- Epigenetic pathway analysis?
- Method to detect DMR
- Filter for mapping quality or for properly paired reads??
- Question about sam output of Bismark
- Methyl-Seq Questions
- Question:Most convenient way to get annotation information for a chromosome location?
- Optimal Setup for MethylMiner-seq (ChIP-seq)
- Comprehensive List of transcription factor binding site databases based on ChIP-Seq
- Input required?
- Insert size for overlapped reads?
- How many inputs for each replicate/cell line
- Will over-amplification during library preparation "drown out" ChIPseq peaks?
- Public Mouse Methyl-seq Data?
- Is it ok to ChIP-Seq two samples when the ChIP worked better in one?
- methylation and genomics variation
- ChIPseq Library Prep Amplification: How many PCR cycles do you use?
- High PCR duplicate with library - possible cause?
- MedIp-seq Input data
- Is methylation data gathered from bisulfite sequencing noisy between biological reps?
- Annotate a bed file from Sureselect Kit(Methylseq)
- MeDIP-seq and compatible DNA adapters for multiplexing?
- Fastqc on Chip-Seq library: confusion
- Searching tool to convert MACS output (chr + coordinates) into genomic feature
- When to integrate the negative control?
- Tools to perform QC of methylation calling
- Is Separose bead protein G sufficient for ChIP-seq analyse?
- How to quantify reads at a location?
- How to build reference genome for targeted region(from a BED file) for alignment?
- Wierd SAM format chromosome column
- MeDIP-sequencing data amount required
- Medip sequencing services
- Can I analyze old blood samples?
- How to deal with biological replicates of nucleosome MNase-seq data?
- Audio Files Transcription
- D. Melanogaster ChIP
- Nice p-value, bad FDR
- For ChIP-seq, maximal coverage at a peak?
- Post-ChIP Sonication Protocol
- MeRIPseq and m6A-seq data processing
- transcription factor binding sites enrichment analysis
- MspI digestion - how is it supposed to look?
- Self designed Methylated Adapters
- which kit to use for whole genome BS-seq library?
- No DNA in ChIP IgG Control - Strange?
- Memory issues running Bismark/Bowtie alignment on a cluster
- ChIP-seq Analysis treated vs. non-treated vs. input controls?
- Directional vs. non-directional sequencing libraries
- CexoR: peak-pair calling in ChIP-exo data with replicates
- DNaseR - DNase-seq digita genomic footprinting in R
- How does MEME-ChIP selects the training set?
- How to do unique mapping in bowtie2
- Methylation Study
- Question about inputs for ChIP-seq
- BSmooth alignment problem
- MiSeq & Bisulphite Sequencing
- Colorspace bis-seq data analysis on Solid
- bsmooth aligner
- read alignment trimming
- Anyone has experience with .ylf (young lab format) files ?
- Target Enrichment from Bisulfite-treated DNA
- Bismark: paired-end low mapping efficiency
- Strange bisulfite libraries
- ChIP-seq library complexity
- Anyone using Bioruptor Pico?
- Unmapped reads (ChIP vs Input)
- statistical analysis of 454 bisulfite sequence data - small sample size
- The highest temperature tolerated by cross-linked chromatin
- Can ChIP Sequencing be used to make exploratory findings about histone methylation?
- MBD qPCR - shift in melt curve
- RRDS adapter mismatch design
- Hands-On Training in DNA Methylation Analysis
- Dangers of Over-amplifying ChIP-Seq Libraries
- Normalization with champ.norm in ChAMP Pakcage
- Problem of methylKit: Too many false positive?
- which kit for RRBS?
- DNase seq
- Chip seq transcription factor low DNA yield
- ChIP-seq
- Help for bisulphite primer design
- ChIPSeq after FACS
- MACS when sonication fragment size is a range of 300 to 700 bp
- Mapping Chip-seq with BWA or Bowtie2?
- Illumina sequencing for multiplexed RRBS
- whole genome bisulfite sequencing in mouse: how many reads required
- ssDNA library prep for meDIP
- Reply from NEB re: ssDNA library prep
- Dynabeads with diagenode magnets?
- ChIPSeq lilbrary prep for Miseq: NEB or TruSeq ?
- Methylation in the + strand influence the expression of gene in the - strand?
- Problems amplifying Ox-BS & BS template from TrueMethyl