eel-pond for mRNAseq

Mention: expect paired end; de novo; first assembly pass.

• 1. Quality Trimming and Filtering Your Sequences
  • Link your data into your working directory
  • Run FastQC on all your files
  • Find the right Illumina adapters
  • Adapter trim each pair of files
  • Interleave the sequences
  • Finishing up
  • Evaluate the quality of your files with FastQC again
• 2. Applying Digital Normalization
  • Run digital normalization
  • Trim off likely erroneous k-mers
• 3. Running the Actual Assembly
  • Build the files to assemble
  • Assembling with Trinity
• 4. Evaluating your transcriptome assembly
  • Transrate
  • BUSCO
• 5. Annotating your transcriptome
  • Install stuff
• 6. Analyzing RNAseq expression with Salmon
  • Run Salmon
• 7. Extracting differentially expressed genes with edgeR

Install and configuration instructions:

• Installation instructions
• Installation and configuration: Amazon Web Services

Indices and tables

• Index
• Module Index
• Search Page

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