Topic outline

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  General

  • Announcements Forum
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  Useful Information about the course

  6 CFU - 48 hours
  
  

  Timetable

  From March 7 to May 30

  Monday 11-13
  Wednesday 14-16
  Thursday 11-13

  
  

  Email is the main vehicle for brief communications in our profession. We are available to meet student for clarification but please mail us for take an appointment!
  

  
  

  
  

  Exam 

  The exam is composed by two parts: write and oral.

  The write part is composed by ALL topics discussed during the lessons, and it will be composed mainly by open questions and exercises.

  In the oral part the student will discuss in ten minutes one scientific paper that the student can be select from all scientific journal papers available by NCBI web site from 2010 till now. The presentation must be clear and well structured, i.e. introduction, scope of the paper, materials and methods used, main results and discussion. The maximum score reachable from this part is 2 points.

  
  

  The final score will be determined by the score reached from the write part plus the score that the student will reach during the oral part (maximum 2 points).

  To access to the oral part is necessary to have passed the write part.

  
  

  Books

  RNA-seq Data Analysis: A Practical Approach Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, Garry Wong

  RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. This book enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes.

  Bioinformatics algorithms  - An active learning approach by Pavel Pevzner and Phillip Compeau

  An Introduction to Bioinformatics algorithms  by Neil C Jones  and Pavel  A. Pevzner
  

  
  
  
  

  • Course Details File
  • Course detailts (Beccuti) File
  • Exam Example File
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  Course Introduction

  • Deep sequencing Introduction File
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  Microarray Technology

  • Microarray File
  • Papers Folder
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  Deep sequencing Technologies

  • DNA instruments history File
  • Library Preparation File
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  Sequence Alignment

  • Introduction to Sequence Alignment File
  • Dynamic programming for Sequence Alignment File
  • Global alignment vs Local alignment File
  • Space efficient sequence alignment File
  • Read mapping File
  • Exercies on Sequence Alignment

  • Exercies on Sequence Alignment File
  • Schema for alignment File
  • Hash table exercise File
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  RNASeq Analysis

  • QualityControl and PCA - Part1 File
  • Coverage and FastQ file format
  • Transcripts Identification File
  • Normalization File
  • Differential Expression Analysis File
  • Paper Folder
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  Interpretation

  • Interpretation File
  • Projects File
  • RNASeqApplications File
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  Clustering algorithms

  • Clustering - Kmeans algorithm File
  • Hierarchical Clustering File
  • R script for clustering File
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  R programming language

  • R - general information File
  • R script for money change File
  • R script for global alignment File
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  Data Analysis in R

  • Dataset PAHCompounds File
  • Dataset SamplesFeatures File
  • Rscript for data analysis File
  • OPECompounds File
  • R Code for OPEs analysis File