Training Notes

Training Notes -- 2018 Spring

上传目录：https://www.jianguoyun.com/p/DbgG1R0Q0NLuBRjG9UY

[Week 8] Differential Expression

[Week 7] Expression Matrix

Schedules for PART II

• Talk about plan and content next Monday:
  1. Basics: Mapping, Annotation and QC
  2. Basics: Expression Matrix
  3. Basics: Differential Expression and Clustering
  4. Normalization (talk about a better way of differential expression)
  5. []Imputation (talk about a better way of clustering)
  6. []Control Data and Extension: RBP, Motif & Structure
• introduce some shared scripts?

Siqi:

1. Talk about sharing
   1. introduced local data being added —>introduce shared/projects/exRNA/README.md, metatable.tsv, google sheet(readonly links)?
   2. sharing on github code and github wiki (shared gitbook removed)

• show and explain snakemake —> show links on gitbook
• sharing programming tips
  • terminal : grey background, Monaco 18
• Homework: comparing gft generated fasta file and miRbase 22 fasta file ( http://www.mirbase.org/ftp.shtml) :

grep  hsa  ~/Downloads/hairpin.fa |wc -l
1917
grep -c ">" RNAs_fasta/miRNA.fa 
1869

Li Yang:

1. Introduce expression terms: RPKM/CPM/...
2. Talk about tools and show example of generating expression matrix

[Week 5-6] Pre-process, mapping, annotation and QC

• 前三周回顾、打分和重新分组： Persons who is not learning for a program
• 演示机器和目录，cpu， top
• 上传目录

[Week 4] ———————— Rest ——————————

[Week 3] 5.Perl/Python

[Week 2] 3.Bash and 4.R

第一节：

1. show github
2. write README
3. show markdown using shared gitbook
4. show PI

• bash

1. tips: cd dir; .bashrc; shortcut
2. tips: ctrl-z, bg; fg; ctrl-c
3. tips: awk

• R

1. yum install
2. explain vector and matrix in R; show google

• Li Yang present Bash and R

第二节

1. 评估作业，explain github, gitbook, upload
2. 1 junior student in each team presents 1) questions (and how they were solved) and 2) tips — ppt and gitbook — 10 min x4

[Week 1] 1.Setup and 2.Linux

目标：

1. SRT项目报名 （3学分）Find 2-3 unders for the real project
2. Group Study
3. Peer learning
4. 3周后测评 3-6 名同学不再继续
5. 最终评定 —》奖品 (team + person)

[Week 0]

• email 选拔

Thank you for interesting in this training course. Please note that this training program will be very intensive. Because we don't have enough resource for all the students, I would need you to input your information in this page first: https://www.icloud.com/numbers/02h27Hq_v76TfHY7USYu4seCg#Bioinfo_Training_Class I will inform you soon if we are able to include you. If you are not included this time, you can always take my course, Introduction to Bioinformatics, next semester.

• email 提醒预习内容

太好了，欢迎你的加入！ 请做好第一节课（周四下午4-6点，生物技术馆一层2-105）的预习：https://lulab.gitbooks.io/bioinfo-training/content/chapter1.html 请带上自己的笔记本，如果是linux系统就直接用；如果是mac或者windows可以事先安装好docker并下载一个linux镜像： https://ygxing.gitbooks.io/docker/content/ （如果没有笔记本，第一节课的时候跟我说一声，给你配置一台。）

• 调研技能水平，预备分组，鼓励预先自由分组：

欢迎大家参加本周四开始的生物信息训练课。 该课程需要大家以小组形式课后练习和讨论，一共分成两个大组，四个小组， 认识的同学先自己找组队一下，周四我在考虑大家意愿的前提下，合理安排每个小组不同年级、不同技能水平的分布。 请大家填一下各自的编程技能水平和年级：https://www.icloud.com/numbers/0w8lKCM1TCgyuLhkk9NykvMrg#Bioinfo_Training_2018