SNAP tutorial | Installation | gene prediction #bioinformatics #tutorial

SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. #snap #geneprediction #bioinformatics #tutorial #bioinfo 1️⃣ Search "SNAP gene prediction" https://github.com/KorfLab/SNAP 2️⃣ Download the whole code SNAP-master.zip 3️⃣ Extract and Compiling make 4️⃣ Check ./snap 5️⃣ Select the geneprediction model from ./HMM directory === mam54-ro.hmm ./snap HMM/mam54-ro.hmm Scerevisiae_Trinity.fasta -aa amino_acid -tx result ✉️Email- [email protected] Email me for further contact 📢 Save my video URL on a notepad in your lab computer. So that you can get this video 📢 Subscribe to my Study tech youtube channel. Because it is free for you but it will help me a lot. ====================== Follow genomic variants analysis pipeline ===================== ------ Tutorial made in the year 2024-2025 🎯Step 1: Download fastq(raw file-SRA) file from NCBI https://youtu.be/LWYQZKRIQKk 🎯Step 2: Fastq file quality check [Fastqc tool] https://youtu.be/URyCysY15mI 🎯Step 3: Trim the adapter and bad reads from the fastq file [Fastp tool] https://youtu.be/SAyerESRrDg 🎯Step 4: Mapping/Alignment of fastq to generate SAM file [STAR tool] https://youtu.be/OD4pBDFXGqY https://youtu.be/0KEaZwoGmg8 🎯Step 5: Sort the SAM file into BAM [ Samtools ] https://youtu.be/T2pE6T8VSBQ 🎯Step 6: AddOrReplaceReadGroup of BAM files [GATK tools] https://youtu.be/vR7nrKpV0f8 🎯Step 7: Mark Duplication of BAM files [GATK tools] https://youtu.be/IPGN4Iy6mw0 🎯Step 8: Merge BAM files [ Samtools ] https://youtu.be/XVmK0G8mQOI 🎯Step 9: mpileup for variant calling [ BCFtools ] https://youtu.be/4fIRQfkbBLo 🎯Step 10: snp analysis [snpEFF tools] https://youtu.be/XyCF2TH6N7M ====================== Subscribe to my channel, and learn complete genomics analysis 💻 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 📢 Guys, if you need any tutorial or help regarding Bioinformatics work, we will try to help you by Video or Chat. Fill free to ask in the 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 snap bioinfo, snap gene prediction, snap tutorial, snap gene prediction tutorial, snap software, snap genome annotation, snap bioinformatics, snap gene prediction tool, snap command line, gene prediction, gene prediction tools, genome annotation, ab initio gene prediction, eukaryotic gene prediction, fungal gene prediction, snap Linux, snap installation, snap ubuntu, snap conda, snap bioconda, command line bioinformatics, genemark training, train genemark, genemark species model, gene prediction fungi, gene prediction plants, gene prediction eukaryotes, snap gene prediction, snap tutorial, snap gene prediction tutorial, snap bioinformatics, genome annotation, gene prediction, ab initio gene prediction, snap linux, snap installation, bioinformatics tutorial, genome annotation tutorial, gene prediction tools, computational biology, genomics tutorial, snap command line, snap fungi, bioinformatics for beginners bioinformatics for beginners, gene prediction explained, genome annotation tutorial, phd bioinformatics, msc bioinformatics, life science bioinformatics, 🏷️ Channel tags transcriptomics, genomics, RNAseq, DNAseq,fasta, fastq, bam, sam, quality control and trimming, bioinformatic tutorial, tutorial,bioinfo, tool, software, package, linux, ubuntu synopsis, script, code, terminal,prompt, command, sequence alignment, sequence, bioinformatics training, file format, bioinformatics projects, #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #ngs #python