[galaxy-user] TopHat to NGS toolbox

[Matthias Dodt]

Hi Rathi!

I wrote a tophat wrapper myself- you can use it if u want, the files are 
attached. you need to adapt the BOWTIE_INDEXES path in the 
toohatwrapper.py and the bowtie path. if these variables are already set 
then you can just remove the lines between "#path settings" and
"#path settings end". And you must include the tophat.xml in the 
tool-conf.xml in the main galaxy folder - in a section of your choice.

Let me know if u find any errors-

greetings

mat

Rathi Thiagarajan schrieb:
> Hello there,
>
> I was really pleased to see that you have the NGS toolbox within Galaxy. I  
> was wondering if there are any plans to include TopHat  
> (http://tophat.cbcb.umd.edu/)and/or Cufflinks  
> (http://cufflinks.cbcb.umd.edu/) into the toolbox as this would be really  
> beneficial.
>
> Also do you have tools to convert fastq format to SAM?
>
> Thanking you in advance.
>
> Cheers,
> Rathi
>   
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