News:GeneSCF (Gene Enrichment Tool): Advice to users

Question

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF)

---------------------- 03/10/2020 ---------------------------

GeneSCF is now moved to GitHub, https://github.com/genescf

Users are recommended to use GeneSCF from our GitHub repository. You are welcome to report your issues on GitHub or on Biostars..

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---------------------- 19/05/2019 ---------------------------

2019/05/19 [23:00 (CEST)]: Due to changes in HTTP's request and response code, GeneSCF has to undergo some minor changes in some of the modules. Downloading updated version solves issues related to database retrieval (prepare_database module).

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

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

If you find GeneSCF as useful and reliable tool please vote on labworm, https://labworm.com/tool/genescf

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---------------------- 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).

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---------------------- 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.

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---------------------- 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'

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---------------------- 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).

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Download: http://genescf.kandurilab.org/downloads.php

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.

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

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[sharmatina189059]

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.

[EagleEye]

Hi,

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').