News: GeneSCF (Gene Enrichment Tool): Advice to users
gravatar for EagleEye
18 months ago by
EagleEye5.5k wrote:

Gene Set Clustering based on Functional annotation (GeneSCF)

---------------------- 11/01/2018 ---------------------------

GeneSCF Twitter

---------------------- 17/08/2017 ---------------------------

If you find GeneSCF as useful and reliable tool please vote on labworm,

---------------------- 01/06/2017 ---------------------------

2017/06/01 [14:15 (CEST)]: Corrected gene id conversion issues (from gene symbols to gene ids) for organisms other than human while performing enrichment analysis with KEGG (not affected for those who used prepare_database module).

---------------------- 03/05/2017 ---------------------------

For Windows 10 bash (version 1607) users: Do not prepare your input gene lists using windows Notepad application. Use Linux text editor like Gedit to prepare and save the list.

---------------------- 09/02/2017 ---------------------------

GeneSCF v1.1 (patch release 2) News : All features are successfully tested on Microsoft Windows 10 bash (version 1607)

  • required installation of 'unzip' utility on windows bash using 'sudo apt-get install unzip'

---------------------- 13/01/2017 ---------------------------

Due to recent changes (naming convention in FTP files) from the database KEGG (01/January/2017) and Gene Ontology (January 2017), the GeneSCF (v1.1 and v1.1-p1) file retrieval utility was unsuccessful with following issues when using update mode (--mode=update),

Example of reported issue: GeneSCF: problem with KEGG annotation

Other possible issues:

  • Creating empty output files

  • Less number of genes mapping to KEGG when using GeneSymbol as input

  • Some organism from Gene Ontology was not supported

The above mentioned issues was faced by GeneSCF v1.1, v1.1-p1 users from 01/January/2017. All the problems are now rectified with new patch release GeneSCF v1.1-p2 (13/January/2017).


Thanks to all users for supporting GeneSCF and please report if there is any problem. We will continue to work on GeneSCF improvements by considering users feedback.


Note: Please always use new (updated) version of GeneSCF.


annotation go kegg news genescf • 1.3k views
ADD COMMENTlink modified 6 months ago • written 18 months ago by EagleEye5.5k

Less number of gene mapping to KEGG database. I have 3652 genes list and I have used following commands. ./prepare_database -db=KEGG -org=acb ./geneSCF -m=update -i=gi_3652 -t= gid -o=/home/tina/geneSCF-master-source-v1.1-p2/output -db=KEGG -p=yes -bg=3652 -org=acb

but only 10 genes have been mapped. I have used different versions of same strain of bacteria.

ADD REPLYlink written 8 months ago by sharmatina18905930


Please provide sample of your input file and output files (including 'gi_3652_user_mapped.list').

Tip: When you run 'prepare_database' before running 'geneSCF', you do not have to run 'geneSCF' in update mode (since you just updated with 'prepare_database').

ADD REPLYlink written 8 months ago by EagleEye5.5k
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