TransDecoder tutorial | Installation | gene prediction #bioinformatics #tutorial

1️⃣ Search "transdecoder" https://github.com/TransDecoder/TransDecoder 2️⃣ Download the whole took TransDecoder-master.zip === check the script from the site https://github.com/TransDecoder/TransDecoder === Visit the project "wiki" for all TransDecoder documentation. 3️⃣ Check ./TransDecoder.LongOrfs -h mkdir output 4️⃣ Find long ORF from the fasta file ./TransDecoder.LongOrfs -t Scerevisiae_Trinity.fasta -m 100 --genetic_code Universal ==== Or you can run this ./TransDecoder.LongOrfs -t Scerevisiae_Trinity.fasta -m 100 --genetic_code Universal --complete_orfs_only === Check the result of in "Scerevisiae_Trinity.fasta.transdecoder_dir" === Make sure that both this dir and "Scerevisiae_Trinity.fasta" are in the same working dir 5️⃣ Coding region prediction ./TransDecoder.Predict -t Scerevisiae_Trinity.fasta ✉️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 transdecoder bioinfo, transdecoder gene prediction, transdecoder tutorial, transdecoder gene prediction tutorial, transdecoder software, transdecoder genome annotation, transdecoder bioinformatics, transdecoder gene prediction tool, transdecoder command line, gene prediction, gene prediction tools, genome annotation, ab initio gene prediction, eukaryotic gene prediction, fungal gene prediction, transdecoder Linux, transdecoder installation, transdecoder ubuntu, transdecoder conda, transdecoder bioconda, command line bioinformatics, genemark training, train genemark, genemark species model, gene prediction fungi, gene prediction plants, gene prediction eukaryotes, transdecoder gene prediction, transdecoder tutorial, transdecoder gene prediction tutorial, transdecoder bioinformatics, genome annotation, gene prediction, ab initio gene prediction, transdecoder linux, transdecoder installation, bioinformatics tutorial, genome annotation tutorial, gene prediction tools, computational biology, genomics tutorial, transdecoder command line, transdecoder 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