Аутор Тема: Биоинформатика за почетнике  (Прочитано 550 пута)

Ван мреже Драган Обреновић

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Биоинформатика за почетнике
« послато: Септембар 23, 2022, 07:41:05 пре подне »
Bioinformatics for Newbies
by Randy Harr with the Consumer WGS Facebook Community

https://docs.google.com/document/d/1Yg4oRDCIQr5RoTZqECPYFDZxoxN-hggXKxy9BVDQpnY/edit

Јако добар увод у биоинформатику и софтверске алате који се користе. Водите рачуна да случајно не мењате online документ (осим ако знате шта радите и због чега предлажете неке измене). Документ је отворен, како би "заједница" могла да предложи додатке, исправке, побољшања и сл. у тексту. Најбоље је да га скинете у .docx формату локално.

Table of Contents
1 Installing Unix / Linux in a Desktop Environment
1.1 Installing in Microsoft Windows environments
1.1.1 Microsoft Windows Subsystem for Linux (WSL)
1.1.2 CygWin (sideways)
1.1.3 Oracle/Sun VirtualBox
1.1.4 VMWare Workstation Player (TBD)
2 Installing Bioinformatics in your Linux Environment
2.1 Installing in Apple MacOS environments
2.2 Installing in Unix / Linux environments
2.3 Installing in your Ubuntu Linux Environment
2.3.1 SAMTools / BCFTools / BWA / FASTQC / FASTP on Ubuntu 18.04
2.3.1.1 Using Ubuntu apt-get
2.3.1.2 Using Anaconda
2.3.2 GATK on Ubuntu 18.04
2.3.3 Picard on Ubuntu 18.04
2.3.4 Other Tools and Resources
3 Processing your DNA files (in dev)
3.1 Getting Your Files From Dante
3.1.1 Renaming your Dante Files
3.2 Already Developed Tools
3.3 Running your own tool flows
3.3.1 File Types and Data Flow
3.3.1.1 Unix File Name Conventions, Compression
3.3.1.2 FASTQ/A
3.3.1.3 BAM/BAI (and SAM, CRAM and CRAI)
3.3.1.4 VCF/gVCF, BCF and TBI (Tabix Index)
3.3.1.5 FA/FNA/FAI
3.3.2 Tool Usage Scenarios
3.3.2.1 Verifying your FASTQ file
3.3.2.1.1 FastQC Tool Approach:
3.3.2.1.2 FastP Tool Approach
3.3.2.1.3 Quick and Dirty Approach
3.3.2.2 Verifying your BAM Average Read Depth and Length
3.3.2.3 Determining your BAM’s reference model used to build it
3.3.2.4 Verifying your VCF file
3.3.2.5 Extracting Y and Mitochondria results from the BAM to a new BAM
3.3.2.6 Creating a BAM from your FASTQ files
3.3.2.7 Creating a VCF from a BAM file (variant calling)
3.3.2.8 Creating a gVCF from your BAM file (variant calling +)
3.3.2.9 Creating a FASTQ from a BAM
3.3.2.10 Remapping a BAM from one Human Genome Model to another
3.3.2.11 Analyzing a VCF file for medical implications
4 Other documents in the series
4.1 Not yet incorporated posts from group and other sources
4.2 References for further reading
5 Appendix 1: Unix / Linux commands