Sequence Analysis

Sequencing technology, Quality control of raw reads, considerations on experimental design for ChIP-seq and RNA sequencing, Read alignment to a reference genome: Bowtie and Tophat, File format conversion and processing: UCSC tools and samtools, Peak calling: MACS, Motif analysis, MEME, Quantification of expression and guided transcriptome assembly: Cufflinks, Analysis of variants. Next generation sequence (NGS) technologies, steps, analysis, application, weaknesses and strengths, key theoretical concepts of alignment and de novo assembly, Use of UNIX for analysis of NGS data.