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For Bioinformatics and NGS Analysis services please contact farhan@jgiconsulting.pk visit: https://jgiconsulting.pk/overview/ #Adapater ...
YouTube-Farhan Haq
How to install Trimmomatic
Checking trimmed fastq file
Quality check of trimmed fastq file
... trimmomatic manual:http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf trimmomatic github page:https ...
YouTube-Bioinformatics Coach
Intro
pc requirement
create a directory and cd into it
Download fastq files
Download the sequence adapter
How to Install Trimmomatic Extract
Run Trimmomatic Command
How to Use the Galaxy Platform for Trimming Paired-End Reads Support My Work https://www.patreon.com/bigdataanalytics ...
Data Preparation
Import the Data
Upload Data
Quality Control
Run the Tool
Module 16: Trim Reads w/ Trimmomatic. 5.9K views · 2 years ago ...more. Hubbard Center for Genome Studies (HCGS).
YouTube-Hubbard Center for Genome Studies (HCGS)
Running Trimmomatic
Delimiting lines with a backslash
Trimmomatic Script Command
Outputs of Trimmomatic
Concatenating Variables
Pathway to Adapters
Sliding Window Trim
Run Trimmomatic in the Background
Examining the output files
In this video, data is loaded via ftp URL and aligned to a built-in genome, hg38.
YouTube-profbiot
Side-loading data
Upload data
FastQC read quality report
Align to reference
Setting up the BWA-MEM tool
Alignment with BWA-MN
What is a genome build?
Downloading the Index
Conclusion
Running Trimmomatic on a cluster Credit by Daniel Ramirez, 2017 This video is part of the DnA Lab short read sequencing workshop run every ...
YouTube-DnA lab short read sequencing workshop
Output and error files
Loading Trimmomatic
Specifying trimmomatic options
Examining the fasta file
Run the batch file
Viewing output files
Viewing trimmed results
In this video we're going to go through some of the different options you have for downloading raw sequence data in fastq format from the ...
YouTube-BabrahamBioinf
How we use public data
Downloading annotated data
Understanding the relationship between GEO and SRA
Downloading SRA data
Sequence databases
Naming the data files
Download SRA Toolkit
Can we use the SRA Toolkit?
Downloading the SRA run table
Future Bitesize Bioinformatics sessions
... ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/NCBI/build37.2/Mus_musculus_NCBI_build37.2.tar.gz Not a fan of doing plugs for ...
YouTube-Alex Soupir
What is STAR?
Read counts
What is an index?
Align to GTF file
Locate GTF file
Run STAR
Output file name prefix
Align reads with STAR
Troubleshooting
RAM usage
Full video clip: https://youtu.be/9o11F1WrHIQ trimmomatic tutorial trimmomatic manual trimmomatic commandline trimmomatic example quality ...
YouTube-Bioinformatics Clips
Specifying spread and width
Specifying the files
Trimmomatic report
... ftp site http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ Install bcftools using anaconda https://youtu.be/BLhVqBXL_v4 Install ...
Prerequisites
Download example vcf file
Download VCF file
Create working directory
Download the data
Index the vcf file
Subset single nucleotide polymorphisms (SNPs)
Subset and get index
23:34. Go to channel · Bioinformatics - Understanding Trimmomatic. Alex Soupir•15K views · 59:20. Go to channel · Alignment and Visualization.
YouTube-Danny Nielsen
Materials and equipment needed
Downloading the data
Aligning reads
... ftp site http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ Install bcftools anaconda: https://youtu.be/BLhVqBXL_v4 building from ...
intro
download the example data
display the chromosome names
save the chromosome names to an output text file
remove duplicate names
count the number of chromosomes
count the total number of variants
subset chromosome list
check for the absence and presence of chromosomes
T-BioInfo - Using FTP and SVL files - Pine Biotech. OmicsLogic · 3:32. Dr. Sharov - Tauber Bioinformatics Research Center - Manifold Learning on ...
YouTube-OmicsLogic
Comments · CLASE Trimmomatic · COMANDOS LINUX · DADA2 CON EL PAQUETE R · How to make FREE Flowcharts & Mind Maps using AI | ChatGPT · Solucionando " ...
YouTube-GENÓMICA Y BIOTECNOLOGÍA Dr. JOSÉ LUIS ACOSTA