lulab/training

Bioinfo Training Program @ Lu Lab

Bioinfo Training @ Lu Lab -- 2018

📖 Tutorial 📖

• ✅ to-do
• ❗️ issues
• 🚩 Basic Tutorial
• 🚩 Advanced Tutorial
• 📖 Additional Tutorial

Scripts and Documents for the training program

• wiki/documents
• scripts/code

DIRs

DIR	Format	Project	Person
shared_scripts	*	intranet/training	Admin
genomes/	fasta, index, gtf/gff	intranet/training	Admin
proj_exRNA/	example files	exRNA	Admin
assets/	*	files for wiki and gitbook	Admin
upload/	*	uploaded scripts	ALL

🎯 Program Summary

3-month training of bioinformatics for Precision Medicine

• Time:   ~3个月, 每周四下午4-6pm （3.15.开始第一次）(calendar)

• Class：生物技术馆一层2-105会议室 (map)

• Target: 10-15人，我们实验室和清华学堂班的部分本科生和低年级研究生;

• Topic: [精准医疗] Identify novel exRNA biomarker for cancer diagnosis;

• Design: 从零基础开始，直到基本机器学习方法，如Feature Selection，的熟练掌握。

Other Scripts and Code

• Shared by PI:Zhi John Lu
• Shared by Ph.D.:Yang Li
• Shared by Ph.D.:Binbin Shi

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Markdown Syntax | Excel Table to Markdown | Paste to Markdown

training's Issues

sam2bam problem

我按照gitbook上面分享的脚本mapping small RNA seq数据，但是从sam 转换成bam文件的时候，提示有以下错误：
W::sam_hdr_parse] Duplicated sequence 'chr1:17368-17436'
[W::sam_hdr_parse] Duplicated sequence 'chr1:30365-30503'
[W::sam_hdr_parse] Duplicated sequence 'chr1:187890-187958'
[W::sam_hdr_parse] Duplicated sequence 'chr1:632324-632413'
[W::sam_hdr_parse] Duplicated sequence 'chr1:1167103-1167198'
请问这个是因为什么？对后续reads length 分布统计会有影响吗？
谢谢！

mapping problem

• 九个sample的mapping: 一开始有的同学结果一样有的不太一样，后来发现和bowtie版本有关，统一了bowtie版本之后都一样了。

• mapping of real data静怡和隆琛重新做mapping，和思琦的不一样