RNA-Seq: GFOLD: a generalized fold change for ranking differentially expressed genes

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GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

Bioinformatics. 2012 Aug 24;

Authors: Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y

Abstract
MOTIVATION: RNA-seq has been widely used to transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the Gene Expression Omnibus (GEO) do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available. RESULTS: We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way GFOLD overcomes the shortcomings of p-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available. AVAILABILITY: The open source C/C++ program is available at http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html CONTACT: X. Shirley Liu - xsliu@jimmy.harvard.edu; Yong Zhang - yzhang@tongji.edu.cn.


PMID: 22923299 [PubMed - as supplied by publisher]



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[IBseq]

Hi,
I just downloaded GFOLD on my unix machine but i'm struggling to understand how to use it.

I am new to unix as well, thus I have no idea what kind of commands should I type to start using GFOLD.

Any help is much appreciated!

irene

[feeldead]

The usage is much like normal unix/linux command. You can first follow the examples in the manual. For example, in the following first command, hg19Ref.gtf is the annotation file. sample1.sam is the mapped reads, and sample1.read_cnt is the output file name. Just replace them with your files/file name.

gfold count -ann hg19Ref.gtf -tag sample1.sam -o sample1.read_cnt
gfold count -ann hg19Ref.gtf -tag sample2.sam -o sample2.read_cnt
gfold diff -s1 sample1 -s2 sample2 -suf .read_cnt -o sample1VSsample2.diff

[bruce01]

Would be interested to try this but just cant get it to install, this might be due to bad GSL install, Im a noob with Linux. Any plans for a Bioconductor package or something easier for me?

[feeldead]

It's not a trivial task to write a user friendly R package. I'm planning it but definitely not planning to make it done immediately.

[bruce01]

Yes I understand, I will see if I can get it to work, I like to try a lot of methods and compare them, this one looks interesting, slightly different. Thanks.

[Parharn]

Have you managed to install it? I installed it and it created gfold exe file, but it is not working and when I type command gfold, it says command not found. Any help?

[Zapages]

I was able to run Gfold without any problems. The first step is to install GSL and then install Gfold


first extract the GSL file in terminal:

-xzf gsl-VERSION.tar.gz

go into the GSL folder:

./configure
make
sudo make install

Then extract the gfold files and run the following code:

g++ -O3 -Wall -lgsl -lgslcblas -g main.cc -o gfold

To run Gfold via terminal in OSX, you'll need to provide the file path to gfold and go from there:

 /User/File/path/gfold1.1.1/gfold

I hope this helps Parharn.

Source:

http://www.brianomeara.info/tutorials/brownie/gsl
http://forums.appleinsider.com/t/868...sl-for-dummies
https://bitbucket.org/feeldead/gfold/

http://compbio.tongji.edu.cn/~fengjx/GFOLD/gfold.html

EDIT: The Tool is now available on iPlant Collaborative for no replicates RNA-Seq reads data set:

Gfold 1.1.1 Counts: https://pods.iplantcollaborative.org...ld+1.1.1+Count

Gfold 1.1.1 DE: https://pods.iplantcollaborative.org...nce+Expression

[TPH]

Hello,
I am trying to install GFOLD into the Linux cluster I am working in. But I keep getting an error message saying g++: command not found
gsl/1.16 is already installed in the cluster. So I loaded the module and tried to execute the following command. The working directory is gsl/1.16/lib/
g++ -O3 -Wall -lgsl -lgslcblas -g /software/gfold.V1.1.2/main.cc -o gfold

Am I doing this in a wrong way? Could anyone please help me to install the package.