mkatari-bioinformatics-august-2013
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Manny's Bioinformatics Workshop
Manny's workshop:
- Introduction to Linux
- Recommended software
- Alan's information about the Cluster Using the cluster
- Alan's information about how to use SLURM Using SLURM
- More notes on shell scripts and writing SLURM batch files More Slurm
wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/v5.0assembly/cassavaV5_0.chromsomesRomanNumerals.fa.gz
ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/annotation/Mesculenta_147_gene.gff3.gz
- Introduction to Sequence Technology
- Introduction to Sequence Alignment
- SNP analysis
- Running samtools mpileup mpileup notes
- Preparing files for GATK and running GATK GATK notes
- Getting snps from a specific region VCF region
- Visualizing your alignments
- Introduction to Mapping and Sequence Assembly
- Introduction to RNA-seq
Manny's R Lectures:
- R Objects and Read/Write Files
- Plotting and Writing Functions in R
- Inferential Statistics using R
- Data cleaning and working with packages
- Differential Gene Expression using DESeq
- Clustering
- GeneSet Enrichment Analysis
mkatari-bioinformatics-august-2013.1433404683.txt.gz · Last modified: 2015/06/04 07:58 by mkatari