Hello,

On the Tophat tool form, if you scroll to the very bottom, the list of implemented option is listed. In general, the order will be the same as the options on the form.


*     Tophat parameter list*
     This is a list of implemented Tophat options:

   -G/--GTF [GTF 2.2 file]           Supply TopHat with a list of gene model 
annotations. TopHat will use the exon records in this file to build a set of 
known splice junctions for each gene, and will attempt to align reads to these 
junctions even if they would not normally be covered by the initial mapping.
   -j/--raw-juncs [juncs file]       Supply TopHat with a list of raw 
junctions. Junctions are specified one per line, in a tab-delimited format. 
Records look like: [chrom] [left] [right] [+/-], left and right are zero-based 
coordinates, and specify the last character of the left sequenced to be spliced 
to the first character of the right sequence, inclusive.
   -no-novel-juncs                   Only look for junctions indicated in the 
supplied GFF file. (ignored without -G)


To set these, change " TopHat settings to use:" to be "Full parameter list" and the form will expand, showing in the full view all of the options.

For these three, the labels are:

   Use Gene Annotation Model:
   Use Raw Junctions:
   Only look for supplied junctions:

Hopefully this helps,

Jen
Galaxy team
On 5/20/13 2:38 PM, Colaneri, Alejandro Cesar wrote:
I want to run tophat with the parameter  "--no-novel-juncs genome"
Where do I find the options to add this parameter?
// //

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