Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013 [2014/06/04 08:08] – mkatari
+++ mkatari-bioinformatics-august-2013 [2014/06/04 08:30] – 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]]
+          * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]]
-  * 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]]
+  * 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]]
+  * 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: