Question: Uploading gbk to galaxy
gravatar for AC
2.9 years ago by
AC0 wrote:


Hi there,

I've been trying to use the GBK-to-GFF3 converter tool from Galaxy/Ratsch Lab by uploading my own GenBank (gbk) file. The drop-menu for "format type" does not have the option to label the file as gbk. I chose the "Auto Detect" function, but the file is being detected as a txt file. The file is in the correct format.

I tried to proceed anyway with the gbk to gaff conversion, but continue to get this error message:

Traceback (most recent call last): File "/data/galaxy/software/oqtans/oqtans_tools/GFFtools/0.2/", line 213, in <module> gbk_parse(gbkfname) File "/data/galaxy/software/oqtans/oqtans_tools/GFFtools/0.2/", line 199, in g


I'm not sure what's going on. Is the labeling of the file format causing the error message, or is there some other issue? I'm new to bioinformatics, so sorry if this is a stupid question.

Btw, can I request that the gbk file format be added to the drop menu in attributes?




galaxy • 888 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by AC0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


It seems you are working with one of Oqtans Galaxy builds?

They offer direct support - see the link above. It is the best way to make requests or get help for the tools/configured builds they publish.

Another alternative, if you just want to do the conversion, is to use the datatype "genbank" and this tool (in your own local): bp_genbank2gff3

Hopefully one of these options works out for you, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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