Recent changes to DeFuse

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:27 -0000

--- v78
+++ v79
@@ -13,6 +13,10 @@
 deFuse has been used to discover gene fusions in tumour samples for the following publications:

 [MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers, Nature 2011](http://www.nature.com/nature/journal/v471/n7338/full/nature09754.html)
+
+## Support
+
+If you are having trouble running deFuse, please post your question to the [deFuse Help](https://sourceforge.net/p/defuse/discussion/deFuseHelp/) forum. 

 ## RNA-Seq Datasets

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:27 -0000

--- v77
+++ v78
@@ -46,8 +46,8 @@
 Improvements:

   * deFuse now takes 2 fastq files as input, replacing the previous archaic input method 
-  * Reimplemented `interrupted_indexN<tt>splicing_indexN`
-  * Optionally compute <tt>interrupted_indexN<tt>splicing_indexN<tt>calculate_extra_annotations 
+  * Reimplemented `interrupted_indexN` and `splicing_indexN`
+  * Optionally compute `interrupted_indexN` and `splicing_indexN` using `calculate_extra_annotations`

 ### Version 0.6.0 is now available

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v76
+++ v77
@@ -37,6 +37,17 @@
 Please feel free to email the author if you have any questions or issues. [[img src=Email.jpg]]

 ## News
+
+### Version 0.6.1 is now available
+
+  * [manual page](DeFuse_Version_0.6.1) 
+  * [source code](http://sourceforge.net/projects/defuse/files/defuse/0.6)
+
+Improvements: 
+
+  * deFuse now takes 2 fastq files as input, replacing the previous archaic input method 
+  * Reimplemented `interrupted_indexN<tt>splicing_indexN`
+  * Optionally compute <tt>interrupted_indexN<tt>splicing_indexN<tt>calculate_extra_annotations 

 ### Version 0.6.0 is now available

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v75
+++ v76
@@ -37,6 +37,30 @@
 Please feel free to email the author if you have any questions or issues. [[img src=Email.jpg]]

 ## News
+
+### Version 0.6.0 is now available
+
+  * [manual page](DeFuse_Version_0.6.0) 
+  * [source code](http://sourceforge.net/projects/defuse/files/defuse/0.6)
+
+Improvements: 
+
+  * Automatic downloading of reference genome and other required files 
+  * Much improved speed due to use of GMAP for the majority of post-process alignments 
+  * Switched back to adaboost as described in the original paper, the svm was occasionally classifying some highly expressed fusions as false 
+
+Bugfixes: 
+
+  * fixed issue with `merge_read_stats.pl`
+
+Other Changes: 
+
+  * no longer filtering garbage reads since it was slow, and generally not useful 
+  * \--mm bowtie option for memory mapped bowtie index was removed from default options, add to `bowtie_options` if in the config if needed 
+
+Comments: 
+
+  * The results for some longer read datasets are greatly improved by trimming a variable number of low quality bases from the ends of each read 

 ### Version 0.5.0 is now available

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v74
+++ v75
@@ -48,6 +48,7 @@
   * Removed overzealous warning: `Fastq error, unable to interpret readid`
   * fixed findcandidatereads crashes 
   * Increased parallelism for faster runtime, especially during split read alignment and spanning read clustering 
+  * removed obsolete break_predict column from output

 No dataset rebuild required.

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v73
+++ v74
@@ -37,6 +37,19 @@
 Please feel free to email the author if you have any questions or issues. [[img src=Email.jpg]]

 ## News
+
+### Version 0.5.0 is now available
+
+  * [manual page](DeFuse_Version_0.4.2) 
+  * [source code](http://sourceforge.net/projects/defuse/files/defuse/0.5)
+
+Fixes the following bugs: 
+
+  * Removed overzealous warning: `Fastq error, unable to interpret readid`
+  * fixed findcandidatereads crashes 
+  * Increased parallelism for faster runtime, especially during split read alignment and spanning read clustering 
+
+No dataset rebuild required. 

 ### Version 0.4.3 is now available

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v72
+++ v73
@@ -43,7 +43,7 @@
   * [manual page](DeFuse_Version_0.4.2) 
   * [source code](http://sourceforge.net/projects/defuse/files/defuse/0.4)

-Added a simulated test dataset and deFuse output based on default parameters [here](https://sourceforge.net/projects/defuse/files/simulation/)
+Added a simulated test dataset and deFuse output based on default parameters [here](http://sourceforge.net/projects/defuse/files/simulation/)

 Fixes the following bugs:

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:26 -0000

--- v71
+++ v72
@@ -37,6 +37,27 @@
 Please feel free to email the author if you have any questions or issues. [[img src=Email.jpg]]

 ## News
+
+### Version 0.4.3 is now available
+
+  * [manual page](DeFuse_Version_0.4.2) 
+  * [source code](http://sourceforge.net/projects/defuse/files/defuse/0.4)
+
+Added a simulated test dataset and deFuse output based on default parameters [here](https://sourceforge.net/projects/defuse/files/simulation/)
+
+Fixes the following bugs: 
+
+  * Inconsequential `Error: expected GTAG and GTC to be same size` message muted 
+  * Removed dependence on human ensembl identifiers to allow for use of mouse genome/gene models 
+  * Warning message when deFuse fails to import any sequence data 
+  * Different read lengths for the same pair no longer fails 
+  * Workaround for occasional samtools merge crash 
+  * Wrong gene annotation bugfix 
+  * Warning for small fragment lengths with discord_read_trim recommendation 
+
+In addition, the script `get_reads.pl` has been added. Pass it the config filename, output directory, and `cluster_id` of a given fusion to view the supporting spanning and split reads. 
+
+No dataset rebuild required. 

 ### Version 0.4.2 is now available

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:25 -0000

DeFuse modified by Andrew

Andrew — Sat, 28 Jun 2014 13:57:25 -0000

--- v69
+++ v70
@@ -37,6 +37,15 @@
 Please feel free to email the author if you have any questions or issues. [[img src=Email.jpg]]

 ## News
+
+### Version 0.4.2 is now available
+
+  * [manual page](DeFuse_Version_0.4.2) 
+  * [source code](http://sourceforge.net/projects/defuse/files/)
+
+Fixes the est island filter that was previously broken. Adds 50 A's to each cDNA sequence to allow for alignment of poly A tail reads. 
+
+Requires a dataset rebuild using the `create_reference_dataset.pl` script. 

 ### Version 0.4.1 is now available