Introduction to NGS data analysis, осень 2013
Курс: Next Generation Sequencing.
Преподаватель: Анна Горбунова.
Даты: Sep 2013 — Dec 2013.
Курс читается в рамках программы "Биоинформатика для биологов".
Программа курса:
- NGS workflows overview: examples, data formats (fasta, fastq, sam/bam, gff, vcf, bed)
- Data pre-processing and QC
- DNA dataflows: re-sequencing. Reference genomes, annotations and data archives
- Aligners: Bowtie and BWA
- SNP and indel callers: Samtools, GATK
- Variant annotations: SnpEff, GATK
- Tumor genome annotations (somatic mutations, germline mutations, LOH, CNV, gene enrichment analysis): VarScan, GSEA
- DNA dataflows: de novo assembly
- RNA dataflows: splice junction analysis, Tophat
- RNA dataflows: absolute expression estimates, Cufflinks, HTSeq
- RNA dataflows: differential expression, Cuffdiff, edgeR
- Bisulfite sequencing: absolute and differential methylation, bsmap, methratio, methylKit
- ChIP-seq dataflows: MACS, peak calling