I want to test several fusion gene detection tools, but am running into a lot of problems only installing them.
I wanted to start this post here to see if other people had similar problems and if we can help each other out. Maybe some of you try to do the same. Any suggestions, ideas, help or critiques are highly welcome!
The tools I'm testing so far are:
- FusionCatcher - easy to install and easy to use, offers a lot of information. Even tests versus virus genomes. Nice tool! Uses different aligners and combines the output. Well documented.
- JAFFA - I got it to run on my data, once the java path was set, it was very easy and straightforward to use
- SoapFuse - Once the folder structure is set, I wrote a shell script for this, it runs. For one week now O_o
- Mapsplice2 - Problems with bowtie index
- FusionMap - Im having problems to prepare the data base, because our proxy won't allow the direct download and the manual downloaded files are not found by the tool...
- EricScript - easy to obtain and to install. downloads everything automatically, however, again when the proxy is blocked you basically cannot use it.
- Trinity - works and is relatively easy to install.With some hiccups, I got it to run.
- snowshoe FTD - asked via mail for the tool, no answer so far
- deFuse - a bit complicated to set up
- fusionQ -
- star-fusion - easy to use and to install.
- tophat-fusion -
- ChimeraScan -
- Bellerophontes -
I'm going to update the list as I go along.
+1 for Fusioncatcher, it's worked well in my hands previously. No tophat-fusion?
I have not tried tophat-fusion yet, because I heard that it is not good and very slow. Do you have any experience with it? I will also add it to the list!