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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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please use the interface at:
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