In this video, I show you how you can analyze Amplicon-sequencing data with a self-created pipeline. FastQ-reads are connected, globally aligned and the results visualized and reported as pdf and html-file.
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Bioinformatic Tools Online - File transfer from the European Nucleotide Archive (ENA)
Bioinformatic tools online - Deeptools: Create Browser Tracks from Bam-files
BWA-aligner
Bioinformatic Tools Online - Oligo alignment
Bioinformatic tools online - Boxplots
Bioinformatic tools online - Heatmaps
Bioinformatic tools online - Venn Diagrams
Bioinformatic tools online - Principal Component Analysis (PCA)
Bioinformatic tools online - Oligo search
Bioinformatic tools online - Result merging
Bioinformatic tools online - Amplicon-sequencing pipeline
Bioinformatic tools online - Running the StringTie pipeline
Bioinformatic tools online - Differential Gene Expression analysis (DESeq2, DESeq, EdgeR)
Bioinformatic tools online - Postprocessing of aligned RNAseq-data
Bioinformatic tools online - Hisat2 for Alignment. Effects of read trimming and program versions
Bioinformatic tools online - Running Trimmomatic to chop reads
Bioinformatic tools online - Running FastQC in various versions
Bioinformatic tools online - Introduction video