Fragment identification and quantification using ChIP-seq
Quantification of histone modification ChIP seq enrichment for data mining and machine learning applications
... gene-wise ChIP-seq enrichment for 20 histone methylations and histone variant ...gene-wise ChIP-seq enrichment can provide significant improvement over strategies that focus on specific genic ...
12
Informative sequence based models for fragment distributions in ChIP seq, RNA seq and ChIP chip data
... During ChIP-seq experiments DNA is extracted from cells, fragmented, and the ends of the fragments are sequenced, generating the sequence ‘tags’ which are used to identify from where in the genome they ...
214
Differential ATAC-seq and ChIP-seq peak detection using ROTS
... very broad peak domains with constant intensity and no clear borders (Figure 3D). Visual inspection of the example loci further illustrates that results of diffReps, PePr and THOR, based on inbuilt candidate peak ...
13
ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
... In ChIP-Seq sample prepara- tion, genomic DNAs are either sonicated or digested into random fragments and size- selected (100-800 bp) for better sequencing ...The ChIP-DNA fragments submit- ted for ...
17
A probabilistic model for competitive DNA binding modeling using ChIP-seq and MNase-seq data
... average fragment size is estimated by the distribution of distances between reads on the positive and negative strands and each read is extended to the average fragment size, while for paired- end ...
48
MUSIC: identification of enriched regions in ChIP Seq experiments using a mappability corrected multiscale signal processing framework
... begin using the length distribution of gene bodies (Figure S3e in Additional file ...marks using l begin = 100, l end = ...the identification of ERs that have a large spectrum of length scales, such ...
15
Identification of ChIP-seq mapped targets of HP1β due to bombesin/GRP receptor activation
... tion using the ChIP-it Express Kit (Active Motif, Carlsbad, ...The ChIP-It control kit “Human” was used as positive ...ed using a Qiagen DNA Micro Kit (Valencia, ...
8
Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows
... We now compare our proposed method FlipFlop to Cufflinks (Trapnell et al., 2010) version 2.0.0, IsoLasso (Li et al., 2011b) version 2.6.1 and NSMAP (Xia et al., 2011) on both simulated and real data. All experiments were ...
16
Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
... enables identification of direct target sequences through the sequencing of RNAs from immunoprecipitated cross-linked Argonaute–miRNA–mRNA complexes [Chi et ...
75
MM ChIP enables integrative analysis of cross platform and between laboratory ChIP chip or ChIP seq data
... performance (Figure S1 in Additional file 1), which underscores the importance of modeling the fragment size of sequenced ChIP-DNA libraries. In the two CTCF datasets described above, the fragment ...
10
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
... performance (Figure S1 in Additional file 1), which underscores the importance of modeling the fragment size of sequenced ChIP-DNA libraries. In the two CTCF datasets described above, the fragment ...
11
Identification of transcription factor binding sites using ATAC seq
... by fragment size, correction of cleavage bias, and signal nor- ...and fragment-size decomposition of cleavage signals as ...TF ChIP-seq dataset for ...
21
Systematic evaluation of factors influencing ChIP-seq fidelity
... DNA using a combination of T4 DNA polymerase, ...large fragment (Klenow polymerase) and T4 polynucleotide ...Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- ‘A’ base for ...
21
Q&A: ChIP-seq technologies and the study of gene regulation
... interaction using formaldehyde as a ...without using a cross-linking agent, and in this case a native ChIP (n- ChIP) without cross-linking might be preferable ...For ChIP of ...
6
Python in ChIP Seq data analysis
... Availability: Source codes are freely available at http://code.google.com/chipseq. _____________________________________________________________________________________________ INTRODUCTION With life sciences becoming ...
6
De novo ChIP seq analysis
... method using human cancer ...novo ChIP-Seq analysis performs as well as peak-calling methods, and in some cases it even slightly improves over alignment based ...
10
Analysis of ChIP-seq data in Galaxy
... • Using the file that MACS generates “MACS peaks on Filter SAM on data 4 “ select only the peaks on chr1. Filter and Sort -> Filter data on any column using simple expressions[r] ...
40
A benchmark for RNA-seq quantification pipelines
... Consistency of isoform calls Because RNA-seq is commonly used to infer alternative transcription, we also assessed the reproducibility of abundance within transcripts of the same gene. To pro- vide a simple and ...
12
A benchmark for RNA seq quantification pipelines
... Consistency of isoform calls Because RNA-seq is commonly used to infer alternative transcription, we also assessed the reproducibility of abundance within transcripts of the same gene. To pro- vide a simple and ...
12
Model based Analysis of ChIP Seq (MACS)
... a ChIP-DNA ...in ChIP-Seq data, espe- cially for activating transcription and epigenetic factors in open ...resulting ChIP-DNA, the true targets may tend to be longer than the background DNA ...
9