Question: extraction DNA sequence using galaxy
gravatar for dev831993
3.1 years ago by
dev8319930 wrote:

How can I extract DNA sequence using galaxy from UCSC if I have their coordinates?  whenever i tried to Fetch sequences for intervals its showing some error like : 

1)There was a conflict when trying to complete your request. 
Error generating display_link: A data display parameter is in the error state: bed_file_for_name
2)No sequences are available for '?', request them by reporting this error.

3)This dataset is in an error state, you cannot view it at an external display application.


what  coordinate region  i submitting is in bed formet:


chr1    10177    10177
chr1    10352    10352
chr1    11007    11008
chr1    11011    11012
chr1    13109    13110
chr1    13115    13116
chr1    13117    13118
chr1    13272    13273
chr1    14463    14464
chr1    14598    14599
chr1    14603    14604

software error galaxy • 862 views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by dev8319930
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


First, assign the database attribute to the dataset if you have not already done so.

Next, if there are no reference liftOver files appearing in the tool, it is possible that either UCSC does not create the indexes for this tool (you can check here: or these have not been incorporated on

The current choice for the latter case is use the tool at UCSC or to startup a local or cloud Galaxy and install the liftOver reference data for use there. No Data Manager for LiftOver installation has been created yet, but the manual set-up is fairly straightforward. Please see:

Best, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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