Nothing is wrong with your job, this is a bug in our code that has been 
corrected. You'll start seeing the correct parameter values again when we 
update our server early next week.

Best,
J.
        
On May 29, 2013, at 11:05 PM, Du, Jianguang wrote:

> Hi All,
> After I finshed Tophat alignment for RNA-seq, I took look at the details of 
> parameters by clicking the icon "View details", and I got the information as 
> shown below:
>  
> Input Parameter       Value   Note for rerun
> RNA-Seq FASTQ file    73: Filtered Groomed data1_rep2 
> Use a built in reference genome or own from your history      indexed 
> Select a reference genome     /galaxy/data/mm9/bowtie_index/mm9       
> Is this library mate-paired?  single  
> TopHat settings to use        full    
> Library Type  FR Unstranded   
> Anchor length (at least 3)    None    
> Maximum number of mismatches that can appear in the anchor region of spliced 
> alignment        None    
> The minimum intron length     None    
> The maximum intron length     None    
> Allow indel search    No      
> Maximum number of alignments to be allowed    None    
> Minimum intron length that may be found during split-segment (default) search 
> None    
> Maximum intron length that may be found during split-segment (default) search 
> None    
> Number of mismatches allowed in the initial read mapping      None    
> Number of mismatches allowed in each segment alignment for reads mapped 
> independently None    
> Minimum length of read segments       None    
> Use Own Junctions     Yes     
> Use Gene Annotation Model     Yes     
> Gene Model Annotations        1: mm9 genes.gtf        
> Use Raw Junctions     No      
> Only look for supplied junctions      No      
> Use Closure Search    No      
> Use Coverage Search   Yes     
> Minimum intron length that may be found during coverage search        None    
> Maximum intron length that may be found during coverage search        None    
> Use Microexon Search  No
>  
> I am totally confused by so many "None"s.
> Then I checked the workflow I set and used for the TopHat alignment, the 
> details are the same as above.
>  
> However, the brief description just under the title of alignment output (. 
> accepted hits) is as below:
>  
> format: bam, database: mm9
> Tophat for Illumina on data 1 and data 73: accepted_hits, TopHat v1.4.0 
> tophat -p 8 -a 8 -m 0 -i 70 -I 500000 -g 20 -G 
> /galaxy/main_pool/pool1/files/004/425/dataset_4425972.dat --library-type 
> fr-unstranded --no-novel-indels --coverage-search --min-cove
>  
> Could you please tell me is there anything wrong (because so many "None" in 
> the detail parameters)?
>  
> Thanks.
> Jianguang DU
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