Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Uploading gbk to galaxy
0
gravatar for AC
2.9 years ago by
AC • 0
AC • 0 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/gbk_to_gff.py", line 213, in <module> gbk_parse(gbkfname) File "/data/galaxy/software/oqtans/oqtans_tools/GFFtools/0.2/gbk_to_gff.py", 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?

Thanks,

AC

 
galaxy • 888 views
ADD COMMENT • link •
modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by AC • 0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It seems you are working with one of Oqtans Galaxy builds? https://wiki.galaxyproject.org/PublicGalaxyServers#Oqtans

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 COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour