Question: GeneSCF: problem with KEGG annotation
2
gravatar for sdum
10 months ago by
sdum20
sdum20 wrote:

Hello, I use geneSCF since several months without problems to annotate human gene list with sym id against GO_all and KEGG databases. However, since some days, I encounter problem with KEGG. The problem occur during the step "Retreving gene list for hsa from KEGG" where I obtain a very very short list of genes mapped (3-4 % rather than I obtain before ~70% with the same list). With the same list with GO_all, there isn't any problem.

Someone have any explanation? Thanks a lot

genescf • 481 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by sdum20
5
gravatar for EagleEye
10 months ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:

Hi,

Sorry for my late response. Although I follow the tag 'genescf', I did not get any alert from Biostars. Just saw your today's email and updated GeneSCF. Now all the issues are solved. Thanks for your valuable feedback.

GeneSCF v1.1 (patch release 2) Fixes - 2017/01/13 Release notes

  • Due to changes (January 2017 release) in source databases KEGG and Gene Ontology, GeneSCF database modules has to be updated to work with recent database releases.

List of solved issues:

1) Empty output files

2) KEGG not working with GeneSymbols

3) Some organisms from Gene Ontology giving errors or not able to process

ADD COMMENTlink modified 10 months ago • written 10 months ago by EagleEye4.8k
0
gravatar for sdum
10 months ago by
sdum20
sdum20 wrote:

Thank you very much!! All is all right now!

ADD COMMENTlink written 10 months ago by sdum20

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

ADD REPLYlink written 10 months ago by WouterDeCoster23k
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