Question: Builtin genome in Galaxy is not displayed in IGB
2
gravatar for morgane.moreau
3.0 years ago by
Australia
morgane.moreau20 wrote:

Hi,

I mapped my peak using MACS in Galaxy using the built-in genome. I can visualize my peaks in IGB via Galaxy but the reference genome is not annotated. If I select my species (E. coli) in IGB, then my peaks (tracks) disappear from the window and data management table. It is the same if I open IGB first, load my reference genome via quickload before viewing my galaxy data. It seems I can't have both.

As soon as I load my bed file, I have the coordinates, but no nucleotide sequence.  I could manually load my UCSC genome, but then the genes have codes, not names.

 

Any help would be much appreciated !

Thank you

 

reference genome igb galaxy • 840 views
ADD COMMENTlink modified 2.9 years ago by Norris, David30 • written 3.0 years ago by morgane.moreau20
2
gravatar for Norris, David
3.0 years ago by
United States
Norris, David30 wrote:

Which genome version in Galaxy did you use to map your reads? IGB currently only has annotation and sequence information available for eschColi_K12. If this is the genome you have been using, please try once more. I have added a mapping from the Galaxy name (i.e. eschColi_K12) to the appropriate IGB genome version name. This new mapping should take effect immediately, and prevent IGB from treating your data as data for an unrecognized genome.

If you are using one of the other options from below you won't be able to view the annotations in IGB without setting up a custom genome. 

Options in Galaxy:

Escherichia coli APEC O1 (eschColi_APEC_O1)
Escherichia coli CFT073 (eschColi_CFT073)
Escherichia coli EC4115 (eschColi_EC4115)
Escherichia coli K12 (eschColi_K12)
Escherichia coli O157:H7 str. Sakai (eschColi_O157H7)
Escherichia coli TW14359 (eschColi_TW14359)
Escherichia coli 536 (16235)
Escherichia coli C str. ATCC 8739 (18083)
Escherichia coli DH10B (20079)
Escherichia coli E24377A (13960)
Escherichia coli HS (13959)
Escherichia coli O157:H7 EDL933 (259)
Escherichia coli SECEC SMS-3-5 (19469)
Escherichia coli UTI89 (16259)
Escherichia coli W3110 (16351)

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Norris, David30
0
gravatar for morgane.moreau
3.0 years ago by
Australia
morgane.moreau20 wrote:

Thank you very much, I was using eschColi_K12, and it is now annotated when I go from galaxy to IGB. However, I can't visualize my peaks.. .any idea why ?

ADD COMMENTlink written 3.0 years ago by morgane.moreau20
0
gravatar for Norris, David
2.9 years ago by
United States
Norris, David30 wrote:

Is it possible your data is using a different name for the chromosomes/contigs than our annotation data? If you can send me the data I am happy to take a look and try to explain what is happening.  

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Norris, David30
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