Differences

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

--- mkatari-bioinformatics-august-2013 [2014/06/10 08:19] – mkatari
+++ mkatari-bioinformatics-august-2013 [2014/07/25 16:31] – mkatari
@@ Line 26: / Line 26: @@
   * SNP analysis
           * [[https://drive.google.com/a/nyu.edu/file/d/0B172nc4dAaaOaDVMUTg5anpmMGs/edit?usp=sharing|Using mpileup on Samtools]]
+          * Preparing files for GATK and running GATK [[mkatari-bioinformatics-august-2013-GATKnotes|GATK notes]]
   * Visualizing your alignments
@@ Line 38: / Line 39: @@
           * [[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://ccb.jhu.edu/software/tophat/manual.shtml|Tophat]]
           * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]]
           * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]]