IGV tool | Install | BAM view | #bioinformatics #biology #tutorial #alignment

--------- IGV tool link https://igv.org/doc/desktop/ https://igv.org/doc/desktop/#DownloadPage/ --------- Download "IGV for linux java included" --------- File name IGV_Linux_2.19.1_WithJava.zip --------- Installation not required --------- Script for open UI (User Interface) IGV tool cd IGV_Linux_2.19.1 ./igv.sh --------- Genome fasta and gtf file sources https://asia.ensembl.org/Saccharomyces_cerevisiae/Info/Index https://ftp.ensembl.org/pub/release-113/fasta/saccharomyces_cerevisiae/dna_index/ https://ftp.ensembl.org/pub/release-113/gtf/saccharomyces_cerevisiae/ --------- Instruction for view BAM file on IGV genome----load genome-----Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa file------load gtf file------ -------- Script for creating index for BAM file ./samtools index ../aligned_sorted.bam ../aligned_sorted.bam.bai # or ./samtools index aligned_sorted.bam aligned_sorted.bam.bai # where the bam file is located in the samtool. ##### See the Samtool tutorial of my channel https://youtu.be/T2pE6T8VSBQ ---------- load file bam file ---------- Note: Bam and bam.bai should be in the same directory/folder ##### See the Bam file generation tutorial of my channel https://youtu.be/OAdXtqrhpCs ---------- System configuration Procession- Intel i5 4th gen, 1.7 GHz, 4 CPU(or thread) RAM-8GB Boot and working drive- 256GB SSD OS- Linux Mint 21.1 Cinnamon -------------------------------- Follow Transcriptome analysis pipeline ------------------------- ------ Tutorial made the year 2024-2025 ------ Learn Download fastq(raw file-SRA) file from NCBI https://youtu.be/7QppKTB-3mQ https://youtu.be/pS1qxUAw5v0 ------ Learn Fastq file quality check https://youtu.be/SAyerESRrDg ------ Learn fastq to Bam file generation https://youtu.be/OAdXtqrhpCs ------ Learn the SAM to BAM file sort by Samtool https://youtu.be/T2pE6T8VSBQ ------ Learn BAM file to Count matrix generation https://youtu.be/62SYrAMRMXc --------------------------------- Subscribe to my channel, and learn complete RNAseq analysis ---- Guys, if you need any tutorial or help regarding Bioinformatics work, we will try to help you by Video or Chat. Fill free to askin comment section. If you are very new to Bioinformatics and have some very basic and silly questions. You are most welcome. Don't hesitate to ask us. You can write in the comment section. --------- Jump to --------- Video specific tags integrative genomics viewer, How to install igv tool, How to run igv tool, igv script, igv terminal, igv tutorial, how to view bam file on igv How to check bam file, igv view igv installation, integrative, genomics, genome,viewer ---------- Channel tags transcriptomics, genomics, RNAseq,DNAseq,fasta,fastq,bam,sam, quality control and trimming, bioinformatic tutorial,tutorial, tool,softwares,linux,ubuntu synopsis,script,code,terminal, sequence alignment, sequence, bioinformatics training, file format, bioinformatics projects, #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #ngs