mkatari-bioinformatics-august-2013
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mkatari-bioinformatics-august-2013 [2014/08/24 11:12] – mkatari | mkatari-bioinformatics-august-2013 [2015/06/17 06:35] – mkatari | ||
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Manny' | Manny' | ||
* Introduction to Linux | * Introduction to Linux | ||
- | * Recommended software | + | * Recommended software |
- | * Recommended software for Apple machines: [[http:// | + | * Windows machines: [[http:// |
+ | * Apple machines: [[http:// | ||
+ | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | ||
* [[https:// | * [[https:// | ||
* Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]] | * Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]] | ||
* Alan's information about how to use SLURM [[using-slurm|Using SLURM]] | * Alan's information about how to use SLURM [[using-slurm|Using SLURM]] | ||
* More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]] | * More notes on shell scripts and writing SLURM batch files [[mkatari-bioinformatics-august-2013-more-slurm|More Slurm]] | ||
- | * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] | + | |
- | * How to use Screen [[mkatari-bioinformatcs-august-2013-ScreenNotes|Screen Notes]] | + | |
- | | + | |
* Introduction to Sequence Technology | * Introduction to Sequence Technology | ||
* [[https:// | * [[https:// | ||
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* SNP analysis | * SNP analysis | ||
* [[https:// | * [[https:// | ||
+ | * Running samtools mpileup [[mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup|mpileup notes]] | ||
* Preparing files for GATK and running GATK [[mkatari-bioinformatics-august-2013-GATKnotes|GATK notes]] | * Preparing files for GATK and running GATK [[mkatari-bioinformatics-august-2013-GATKnotes|GATK notes]] | ||
+ | * Getting snps from a specific region [[mkatari-bioinformatics-august-2013-VCFregion|VCF region]] | ||
* Visualizing your alignments | * Visualizing your alignments | ||
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* R Objects and Read/Write Files | * R Objects and Read/Write Files | ||
- | * [[https://docs.google.com/ | + | * [[https://drive.google.com/ |
* [[https:// | * [[https:// | ||
+ | * [[https:// | ||
* [[https:// | * [[https:// | ||
* [[https:// | * [[https:// | ||
* Plotting and Writing Functions in R | * Plotting and Writing Functions in R | ||
- | * [[https://docs.google.com/ | + | * [[https://drive.google.com/ |
* [[https:// | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
* Inferential Statistics using R | * Inferential Statistics using R | ||
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* Differential Gene Expression using DESeq | * Differential Gene Expression using DESeq | ||
+ | * [[https:// | ||
* [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]] | ||
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari