| Topic |
Description |
Tools |
- Introduction
|
- Data Types, data formats -(Fastq, Qseq etc. most of the types including color space)
- Understanding raw read data from the NGS sequencers
|
- Understanding NCBI, PUBMED,MESH and CDD
|
NCBI, PUBMED,MESH and CDD |
- Sequence alignment and its application
|
- Introduction
- Algorithms
- Multiple sequence alignment
|
- BLAST
- FASTA
- Needleman wunch
- Smith waterman
- Clustal omega
- t-coffee
|
- Genomics
|
- Introduction with gene databases-GENE, SNP
- Genome Annotation and Visualization
- Gene finding and function prediction
- General introduction to Gene expression in prokaryotes and eukaryotes, transcription factors Binding sites ( SNP, EST, STS)
|
GENSCAN |
-
ORF finder and its application
|
Online tools with ORF |
ORF finder |
- Gene Prediction AND Expression
|
- Introduction to gene and gene prediction
- Determine Beginning and end positions of gene in genome and gene structure
- Codons; Discovery of split genes; Exons and Introns; Splicing;
|
- Human Splicing finder
- GenMark and GenScan
|
- Phylogenetic tree-detail
|
- Definitions of homologues, orthologues, paralogues
- Methods of phylogenetic analysis: UPGMA, WPGMA, neighbour joining method, Maximum likelihood
|
- PHYLIP
- MEGA
- Tree finder
|
- Next Generation Sequencing Technology
|
- What is NGS? And Basic concepts
- Sequencing Methods
- Platform overview and
- Biological applications
- Recent scientific breakthroughs using NGS technology
- Applications
|
- Illumina hi seq
- mi seq
- phylogenetic analysis
- MUMmer 3.12
|
- Introduction to Sequencing
|
- Traditional Methods
- Sanger sequencing
- Drawbacks of Sanger’s sequencing
|
|
- NGS Data Generation
|
- Generation of large scale molecular biology data
|
|
- Next Generation Sequencing Methods
|
- Concept of sequence quality scores (Overview of Phred, Illumina, SoliD sequencing)
- Issues and Filtering Next-Gen data (coverage, depth, short-reads, Chimeras)
- Emulsion based PCR and polonies
- SAM tools and SAM alignment format
- Single molecules sequencing methods.
- Applications of High throughput sequencing methods.
|
- NGS Data Analysis
|
- Alignment and mapping highlighting differences with conventional alignment, tools used and brief parameters (BWA, Bowtie, MAQ, etc)
- Brief Concepts of
- ChiP-seq,
- DNase-seq,
- MNase-seq,
- RNA-seq.
- Transcript Assembly and gene expression (RNA-Seq) with tools like Tophat/Cufflinks
- Variation detection (DNA-Seq and Exome sequencing)
- Protein Binding Site detection (Chip-Seq) with tools like MACS
- CpG Islands and Methylaion Patterns (Bisu lphite-Seq) with tools like bismark
|
- Genome Databases and File Formats
|
- Databases
- File formats
|
- GENEBANK
- GENE
- SNP
- fast q
- gbk
|
- Galaxy
|
- How to upload data
- Explore published histories
- Generate new history
- Changing dataset formats and editing attributes
|
- SRA data FTP download
- SAM tools
|
- Data processing
|
- Analysis workflow
- Sequence quality evaluation
- Alignment theories
- Data formats and Data visualization to explore various NGS nodes
|
- FastQC
- BLAST All
- Stand alone
- Blast
- SAM tools
- Bed Format
|
- DNA-Seq
|
- Genetic variation
- Variant Calling using various methods
- Variant Annotations
|
- GATK
- Snver
- VarScan
- Picard
- SAMtool
|
- RNA-Seq
|
- Biological theories on RNA-Seq experiments
- Alignment
- Gene expression analysis
- Alternative splicing
- Transcript variation
- Allele-specific expression
|
- BlAST All
- Standalone blast
|
- ChIP-seq
|
- Biological theories on ChIP-seq analysis
- DNA fragment evaluation
- Peak identification
|
- Trimmomatic
- FAST QC
|
- NGS Data Visualization with Exploration with IGV
|
- View, Navigate and Browse large dataset
- Visualize specific region on Genome and View Alignment
|
BLAST |
