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mkatari-bioinformatics-august-2013
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Alan Orth
Jean-Baka Domelevo Entfellner
mkatari-bioinformatics-august-2013
Manny's Bioinformatics Workshop
Manny's workshop:
Introduction to Linux
Recommended software
Windows machines:
MobaXterm
Apple machines:
Xquartz
Linux notes
ppt
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
Introduction to Sequence Technology
ppt (updated Aug 22, 2014)
Fastx toolkit
Fastqc
Introduction to Sequence Alignment
ppt
Blast notes
Bowtie notes
Samtools
MUMmer
SNP analysis
Using mpileup on Samtools
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
IGVnotes
Introduction to Mapping and Sequence Assembly
ppt
Velvet Documentation
ABySS
Introduction to RNA-seq
ppt
Bowtie2
Tophat
Cufflinks
CuffDiff
DESeq manual
Manny's R Lectures:
R Objects and Read/Write Files
ppt
Exercise 1
Worksheet 1
example.txt
example.csv
Writing Functions in R
ppt
Normalized Data
Worksheet 2
genes5expvalues
Introduction to Statistics
ppt
Plotting using R
ppt
breast cancer dataset
Worksheet 3
Volcano plot
Data cleaning and working with packages
Next-gen workflow
Bioconductor
Example file
Clean SNP data
Convert SNP File format
Differential Gene Expression using DESeq
RNA-seq
DESeq
Clustering and GeneSet Enrichment analysis
ppt
Clustering
Loading Phytozome data
Notes to convert Phytozome Data to GOStats
mkatari-bioinformatics-august-2013.txt
· Last modified: 2017/01/25 05:13 by
mkatari
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