RNA-seq Analysis (in Linux)
Channel: Codanics
Date: 2023-02-04

#bioinformatics #rnaseq #genomic 

Here are the time stamps:
00:00:00 Intro to RNAseq
00:03:27 Start the Linux system
00:06:19 Add the channels in anaconda.
00:06:41 Creating Env for redemption
00:07:42 Install the reademption conda package.
00:09:53 How to make most of this session.
00:10:48 Central Dogma
00:12:01 Exons are important.
00:15:24 RNA-seq
00:22:12 Timeline of sequencing technologies
00:24:09 Bioinformatics tools used in RNA-seq analysis.
00:25:41 Check quality
00:26:50 Preprocessing
00:29:03 Alignment
00:38:53 Expression Quantification
01:00:04 Complete code for reademption
01:03:25 Illumina sequencing machines
01:14:33 Time and money spent in genomics experiment.
01:17:38 Fastq file
01:27:10 Tools for quality control
01:30:37 Creating env for RNA-seq
01:31:50 installing python.
01:32:34 Installing fastqc
01:36:18 Installing multiqc
01:37:37 checking fastqc
01:39:07 Checking reads online through sra
01:39:07 Downloading reads through SRR number
01:50:18 Installing Grabseqs
01:56:33 command for trimming from fastp
02:01:30 Fasta file
02:01:09 file formats
02:04:27 Illumina sequences are short for a reason
02:09:30 creating new environment for gradseq  
02:10:00 files in SRA Project
02:13:50 Normalization
02:18:43 Experimental planning
02:19:50 Study design  
02:26:50 Sequencing
02:27:39 Deeper Sequencing or more replicate
02:35:31 How many replicates are needed in RNA-seq experiment.
02:42:45 Single end VS paired end reads.
02:49:44 cost of sequencing
02:53:13 Long read sequencing technologies.
02:56:48 Library preparation
03:00:52 Decision tree for RNAseq library preparation
03:12:19 Checking how to download SRR file using grabseq
03:20:52 fasterq-dump