ChIP-Seq Analysis
ChIP-Seq, or chromatin immunoprecipitation sequencing, is a technique that performs analysis of transcriptome data generated by next-generation sequencing technologies or by microarrays. A success in analysis of transcriptome is largely dependent on bioinformatics tools developed to support the different steps in the process.
The ChIP-Seq section of T-BioInfo provides a flexible approach to analysis of transcriptome data with a number of known and new algorithms (“modules”) included and specially designed analysis features.
The analysis pipelines go across the twelve different functional sections (analysis stages) found on the interactive graph, which will process your data from start to finish by utilizing the section specific algorithms (modules). Starting from left to right these sections are:
- Data Pre-Processing: cleaning the primers in raw reads and format transfer; Result: cleaned NGS data or array data represented as NGS pseudo-reads.
- Data Simulation: expression of isoforms of genes is simulated; Result: artificial NGS data with introduces errors representing expression of pre-defined splice variants.
- Error Correction: correction of sequencing errors: Result: about 75% of the sequencing errors will be corrected
- Mapping on Genome: alignment of reads against reference genome or mRNAs; Result: alignments of reads against references
- Transformation:
- Normalization:
- Background (Genome):
- Bins:
- Segmentation:
- Mappability:
- Pick Extension:
- TF-Binding:
- Integration:
Thus, a typical workflow might look like this
- Simulation of isoform expression or input of real NGS/array data
- Quality control your data and error/artifact correction
- Mapping Reads
- Determining of expressed isoforms of genes
- Counting Reads per genome element: gene and isoform expressions
- Differential expression across biological conditions and statistical analysis