Metagenomic Annotation WorkshopΒΆ
In this part of the metagenomics workshop we will:
- Translate nucleotides into amino acid seuquences using EMBOSS
- Annotate metagenomic reads with Pfam domains
- Discuss and perform normalization of metagenomic counts
- Take a look at different gene abundance analysis
The workshop has the following exercises:
- Translation Exercise
- HMMER Exercise
- Normalization Exercise
- Differential Exercise
- BonusExercise: Metaxa2
At least a basic knowledge of how to work with the command line is required otherwise it will be very difficult to follow some of the examples. Have fun!
Contents:
- Checking required software
- Translating nucleotide sequences into amino acid sequences
- Search amino acid sequences with HMMER against the Pfam database
- Normalization of count data from the metagenomic data sets
- Estimating differentially abundant protein families in the metagenomes
- Bonus exercise: Using Metaxa2 to investigate the taxonomic content