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mkatari-bioinformatics-august-2013 [2014/06/10 08:17] – mkatarimkatari-bioinformatics-august-2013 [2016/08/15 08:15] – mkatari
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 Manny's workshop: Manny's workshop:
   * Introduction to Linux   * Introduction to Linux
-          * Recommended software for Windows machines: [[http://mobaxterm.mobatek.net/|MobaXterm]] +          * Recommended software  
-          * Recommended software for Apple machines: [[http://xquartz.macosforge.org/landing/|Xquartz]]+                    * Windows machines: [[http://mobaxterm.mobatek.net/|MobaXterm]] 
 +                    * Apple machines: [[http://xquartz.macosforge.org/landing/|Xquartz]] 
 +          * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]] 
           * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]]
           * 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://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]]+          * [[https://drive.google.com/file/d/0B172nc4dAaaOUGNYRFFfN1ZLOUk/edit?usp=sharing|ppt (updated Aug 22, 2014)]]
           * [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]]           * [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]]
           * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]           * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]
 +
   * Introduction to Sequence Alignment   * Introduction to Sequence Alignment
           * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]
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           * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]           * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]
           * [[http://mummer.sourceforge.net/manual/|MUMmer]]           * [[http://mummer.sourceforge.net/manual/|MUMmer]]
 +
   * SNP analysis   * SNP analysis
           * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]           * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]
 +          * 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]]
 +          * Getting snps from a specific region [[mkatari-bioinformatics-august-2013-VCFregion|VCF region]]
  
   * Visualizing your alignments   * Visualizing your alignments
           * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]           * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]
 +
   * Introduction to Mapping and Sequence Assembly   * Introduction to Mapping and Sequence Assembly
           * [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]]
           * [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]]           * [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]]
           * [[http://seqanswers.com/wiki/ABySS|ABySS]]           * [[http://seqanswers.com/wiki/ABySS|ABySS]]
 +
   * Introduction to RNA-seq   * Introduction to RNA-seq
           * [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]]
           * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]]           * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]]
-          * [[http://tophat.cbcb.umd.edu/manual.shtml|Tophat]]+          * [[http://ccb.jhu.edu/software/tophat/manual.shtml|Tophat]]
           * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]]           * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]]
           * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]]           * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]]
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 Manny's R Lectures: Manny's R Lectures:
 +
   * R Objects and Read/Write Files   * R Objects and Read/Write Files
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]]+          * [[https://drive.google.com/file/d/0B172nc4dAaaOU3BHbXJQYUp4ajg/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]]
 +          * [[https://drive.google.com/file/d/0B172nc4dAaaOcENCal94M0JMVGc/view?usp=sharing|Worksheet 1]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]
-  * Plotting and Writing Functions in R + 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]]+  * Writing Functions in R 
 +          * [[https://drive.google.com/file/d/0B172nc4dAaaOb0t0MWo5ZDRFY2c/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
-  * Inferential Statistics using R +          * [[https://drive.google.com/file/d/0B172nc4dAaaOakNfZTA3OHdfbU0/view?usp=sharing|Worksheet 2]] 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]]+          * [[https://drive.google.com/open?id=0B172nc4dAaaOZHVlYk1oODl3cE0&authuser=1|genes5expvalues]] 
 + 
 +  * Plotting using R 
 +          * [[https://drive.google.com/file/d/0B172nc4dAaaOWlh0VUlPTW5RS2c/view?usp=sharing|ppt]]
           * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]]           * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]]
 +          * [[https://drive.google.com/file/d/0B172nc4dAaaOYXJoeTB2ZEg5Rm8/view?usp=sharing|Worksheet 3]]
           * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]           * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]
 +
   * Data cleaning and working with packages   * Data cleaning and working with packages
           * [[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/|Next-gen workflow]]           * [[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/|Next-gen workflow]]
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           * [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]]           * [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]]
           * [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]]           * [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]]
 +
   * Differential Gene Expression using DESeq   * Differential Gene Expression using DESeq
 +          * [[https://drive.google.com/open?id=0B172nc4dAaaOaU82cHVNTkJ2RGM&authuser=1|RNA-seq]]
           * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]           * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]
-  * Clustering + 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]]+  * Clustering and GeneSet Enrichment analysis 
 +          * [[https://drive.google.com/open?id=0B172nc4dAaaOWXRMdU1sMGlLR2M&authuser=1|ppt]]
           * [[mkatari-bioinformatics-august-2013-clustering|Clustering]]           * [[mkatari-bioinformatics-august-2013-clustering|Clustering]]
-  * GeneSet Enrichment Analysis 
-          * [[https://docs.google.com/file/d/0B172nc4dAaaOcnVlM25nWk1ZVWs/edit?usp=sharing|ppt]] 
           * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]           * [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]
 +          * [[mkatari-bioinformatics-august-2013-Phytozome2GoStats|Notes to convert Phytozome Data to GOStats]]
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari