Recent changes to Home

Home modified by elizabeth henaff

elizabeth henaff — Thu, 30 Jul 2015 00:46:55 -0000

--- v2
+++ v3
@@ -1,4 +1,3 @@
-
 Summary
 -------

@@ -13,7 +12,7 @@

 ~~~~~~~~
 // clone the repository
-git clone ssh://git.code.sf.net/p/jitterbug/code jitterbug-code
+git clone git://git.code.sf.net/p/jitterbug/code jitterbug-code

 //list the available tags
 git tag -l

Home modified by elizabeth henaff

elizabeth henaff — Thu, 30 Jul 2015 00:39:52 -0000

--- v1
+++ v2
@@ -1,8 +1,32 @@
-Welcome to your wiki!

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+Summary
+-------

-The wiki uses [Markdown](/p/jitterbug/wiki/markdown_syntax/) syntax.
+This set of programs allows one to identify transposable element insertions (TEI) in a sequenced sample with respect to an assembled reference. 
+
+The main script jitterbug.py performs this analysis, using a .bam file of mapped reads and the annotation of TEs in the reference.
+
+Additional modules are provided to filter and plot these results, compare tumor/normal pairs as well evaluate predictions from simulated data. 
+
+To access the release version corresponding to the related publication in BMC Genomics:
+
+
+~~~~~~~~
+// clone the repository
+git clone ssh://git.code.sf.net/p/jitterbug/code jitterbug-code
+
+//list the available tags
+git tag -l
+
+//move to the version tagged with v1.0
+git checkout tags/v1.0
+~~~~~~~~
+
+
+Information on dependencies, installation and usage are available in that version's README
+
+Enjoy! 
+

 [[project_admins]]
 [[download_button]]

WikiPage Home modified by elizabeth henaff

elizabeth henaff — Wed, 22 Feb 2012 14:13:59 -0000

Welcome to your wiki! This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/jitterbug/wiki/markdown_syntax/) syntax. [[project_admins]] [[download_button]]