How I perform Genome Mapping using BWA | Mapping any Reads to a Reference Genome | Paired-end Reads

Bioinformatics Coach
Bioinformatics Coach
11.2 هزار بار بازدید - 2 سال پیش - This tutorial shows you how
This tutorial shows you how to perform genome mapping using Burrows-Wheeler Aligner(BWA) and process the output bam file using samtools.

Script and data can be downloaded from here: Patreon: 75872047

Dealing with multiple samples: Patreon: genome-mapping-77559127

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Commands used in this tutorial
bwa index
bwa mem
samtools view
samtools sort
samtools index
samtools flagstat


Course materials
   reference genome: https://www.ncbi.nlm.nih.gov/nuccore/...
   source of data: https://www.ncbi.nlm.nih.gov/pmc/arti...
   sra-database https://trace.ncbi.nlm.nih.gov/Traces...
   download link for read 1  http://ftp.sra.ebi.ac.uk/vol1/run/ERR...
   download link for read 2   http://ftp.sra.ebi.ac.uk/vol1/run/ERR...

BWA home page
 https://github.com/lh3/bwa
 http://bio-bwa.sourceforge.net/

samtools
 https://github.com/bahlolab/bioinfoto...
  http://www.htslib.org/doc/samtools-fl...

How to install BWA
   build from source: Bioinformatics Genome Mapping Tools| ...
   use binaries: Bioinformatics Tools | How to Install...
   use conda: Bioinformatics Tools | How to Install...

How to Install samtools
   binaries:Bioinformatics Tools | Install samtoo...
   build from source:Bioinformatics Tools | Install samtoo...
   use conda:Bioinformatics Tools | Install samtoo...


Chapters
00:00 Intro
00:13 PC Requirement
00:43 Data Description
00:58 Download data
01:33 Open terminal
01:42 Create a working directory
01:57 Download data
03:19 Download the reference sequence
04:27 Index the reference sequence
05:50 Map reads to the reference sequence
13:01 Index the bam file
14:11 Check the mapping statistics




#bioinformatics #bioinformática #bioinformaticsforbeginners #genomics

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2 سال پیش در تاریخ 1401/04/01 منتشر شده است.
11,228 بـار بازدید شده
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