How I perform Genome Mapping using BWA | Mapping any Reads to a Reference Genome | Paired-end Reads
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
Support my work
https://www.buymeacoffee.com/informat...
https://www.paypal.com/paypalme/thein...
Patreon: bigdataanalytics
One-on-One coaching (Video Conferencing)
https://calendly.com/bioinformaticscoach
One-on-One coaching(Audio Call)
https://clarity.fm/vincentappiah
Get more bioinformatics tutorials on Patreon
Patreon: bigdataanalytics
Subscribe to my channels
Bioinformatics: @bioinformaticscoach
Data Science: @datasciencecoach
Short Clips: @bioinformaticscforbeginners
Reach out
[email protected] my work
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
DNA Icon by flaticon
Script and data can be downloaded from here: Patreon: 75872047
Dealing with multiple samples: Patreon: genome-mapping-77559127
Support my work
https://www.buymeacoffee.com/informat...
https://www.paypal.com/paypalme/thein...
Patreon: bigdataanalytics
One-on-One coaching (Video Conferencing)
https://calendly.com/bioinformaticscoach
One-on-One coaching(Audio Call)
https://clarity.fm/vincentappiah
Get more bioinformatics tutorials on Patreon
Patreon: bigdataanalytics
Subscribe to my channels
Bioinformatics: @bioinformaticscoach
Data Science: @datasciencecoach
Short Clips: @bioinformaticscforbeginners
Reach out
[email protected] my work
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
DNA Icon by flaticon
2 سال پیش
در تاریخ 1401/04/01 منتشر شده
است.
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