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 ParameterValueNote for rerun
RNA-Seq FASTQ file73: Filtered Groomed data1_rep2
Use a built in reference genome or own from your historyindexed
Select a reference genome/galaxy/data/mm9/bowtie_index/mm9
Is this library mate-paired?single
TopHat settings to usefull
Library TypeFR Unstranded
Anchor length (at least 3)None
Maximum number of mismatches that can appear in the anchor region of spliced alignmentNone
The minimum intron lengthNone
The maximum intron lengthNone
Allow indel searchNo
Maximum number of alignments to be allowedNone
Minimum intron length that may be found during split-segment (default) searchNone
Maximum intron length that may be found during split-segment (default) searchNone
Number of mismatches allowed in the initial read mappingNone
Number of mismatches allowed in each segment alignment for reads mapped independentlyNone
Minimum length of read segmentsNone
Use Own JunctionsYes
Use Gene Annotation ModelYes
Gene Model Annotations1: mm9 genes.gtf
Use Raw JunctionsNo
Only look for supplied junctionsNo
Use Closure SearchNo
Use Coverage SearchYes
Minimum intron length that may be found during coverage searchNone
Maximum intron length that may be found during coverage searchNone
Use Microexon SearchNo

 

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: 
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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