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--- mkatari-bioinformatics-august-2013 [2014/06/04 08:08] – mkatari
+++ mkatari-bioinformatics-august-2013 [2014/06/10 08:17] – mkatari
@@ Line 2: / Line 2: @@
 Manny's workshop:
-  * Introduction to Linux -- [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]]
+  * Introduction to Linux
-  * Introduction to Sequence Technology -- [[https://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]] -- [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]] -- [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]
+          * Recommended software for Windows machines: [[http://mobaxterm.mobatek.net/|MobaXterm]]
-  * Introduction to Sequence Alignment -- [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-BlastNotes|Blast notes]] -- [[mkatari-bioinformatics-august-2013-BowtieNotes|Bowtie notes]] -- [[http://samtools.sourceforge.net/samtools.shtml|Samtools]] -- [[http://mummer.sourceforge.net/manual/|MUMmer]]
+          * Recommended software for Apple machines: [[http://xquartz.macosforge.org/landing/|Xquartz]]
-  * Visualizing your alignments -- [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]]
-  * Introduction to Mapping and Sequence Assembly -- [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]] -- [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]] -- [[http://seqanswers.com/wiki/ABySS|ABySS]]
+          * Alan's information about the Cluster [[[[using-the-cluster|Using the cluster]]
-  * Introduction to RNA-seq -- [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]] -- [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]] -- [[http://tophat.cbcb.umd.edu/manual.shtml|Tophat]] -- [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]] -- [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]] -- [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]]
+          * 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]]
+          * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]]
+          * How to use Screen [[mkatari-bioinformatcs-august-2013-ScreenNotes|Screen Notes]]
+  * Introduction to Sequence Technology
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]]
+          * [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]]
+          * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]
+  * Introduction to Sequence Alignment
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]
+          * [[mkatari-bioinformatics-august-2013-BlastNotes|Blast notes]]
+          * [[mkatari-bioinformatics-august-2013-BowtieNotes|Bowtie notes]]
+          * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]
+          * [[http://mummer.sourceforge.net/manual/|MUMmer]]
+  * SNP analysis
+          * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]
+  * Visualizing your alignments
+          * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]]
+  * Introduction to Mapping and Sequence Assembly
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]]
+          * [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]]
+          * [[http://seqanswers.com/wiki/ABySS|ABySS]]
+  * Introduction to RNA-seq
+          * [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]]
+          * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]]
+          * [[http://tophat.cbcb.umd.edu/manual.shtml|Tophat]]
+          * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]]
+          * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]]
+          * [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]]
 Manny's R Lectures:
-  * R Objects and Read/Write Files -- [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]
+  * R Objects and Read/Write Files
-  * Plotting and Writing Functions in R -- [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOZENzZGFNVEp5WTA/edit?usp=sharing|ppt]]
-  * Inferential Statistics using R -- [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]] -- [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]] -- [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOS29XcEJyU0h0SlU/edit?usp=sharing|Exercise 1]]
-  * Data cleaning and working with packages -- [[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/|Next-gen workflow]] -- [[http://bioconductor.org|Bioconductor]] -- [[https://docs.google.com/file/d/0B172nc4dAaaOMG44Zk1BT2NFdkU/edit?usp=sharing| Example file]] -- -- [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]] -- -- [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOTElDZkIwTUdqWU0/edit?usp=sharing|example.txt]]
-  * Differential Gene Expression using DESeq -- [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOemFPcWprQm9IeWc/edit?usp=sharing|example.csv]]
-  * Clustering -- [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-clustering|Clustering]]
+  * Plotting and Writing Functions in R
-  * GeneSet Enrichment Analysis -- [[https://docs.google.com/file/d/0B172nc4dAaaOcnVlM25nWk1ZVWs/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-LoadingPhytozome|Loading Phytozome data]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOZ1ZoekZwcWZtT28/edit?usp=sharing|ppt]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOSS1hOFBxMWk0eEE/edit?usp=sharing|breast cancer dataset]]
+  * Inferential Statistics using R
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOQTFjWDJJWGxLUWM/edit?usp=sharing|ppt]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaONlZ4QXByRThPNXM/edit?usp=sharing|Normalized Data]]
+          * [[mkatari-bioinformatics-august-2013-volcano-plot|Volcano plot]]
+  * Data cleaning and working with packages
+          * [[http://www.bioconductor.org/help/workflows/high-throughput-sequencing/|Next-gen workflow]]
+          * [[http://bioconductor.org|Bioconductor]]
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOMG44Zk1BT2NFdkU/edit?usp=sharing|Example file]]
+          * [[mkatari-bioinformatics-august-2013-cleanSNP |Clean SNP data]]
+          * [[mkatari-bioinformatics-august-2013-convert-SNP|Convert SNP File format]]
+  * Differential Gene Expression using DESeq
+          * [[mkatari-bioinformatics-august-2013-DESeq|DESeq]]
+  * Clustering
+          * [[https://docs.google.com/file/d/0B172nc4dAaaOaC16N25EU01iXzg/edit?usp=sharing|ppt]]
+          * [[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]]