Steps to convert GFF file to GTF file

1. First, you need to install the Cufflinks software:

Execute the command: gff read **.gff  -T -o **. gtf    

For example: gffread test.gff -T -o test.gtf

Steps to install Cufflinks:

1. In order to install Cufflinks , the Boost C++ libraries must be available . Download Boost and install it. It is installed in /usr/local by default .

    $ tar jxvf boost_1_53_0.tar.bz2

    $ cd boost_1_53_0

    $ ./bootstrap.sh

    $ sudo ./b2 install

2. Install SAM tools (the detailed installation steps of samtool have been introduced earlier) .

    $ tar jxvf samtools-0.1.18.tar.bz2

    d cd samtools-0.1.18

    $ make

    $ sudo su 

    # mkdir /usr/local/include/bam

    # cp libbam.a /usr/local/lib

    # cp *.h /usr/local/include/bam/

    # cp samtools / usr / bin /

3. Install  Eigen libraries .

 Download Eigen

   $ tar jxvf 3.1.2.tar.bz2

   $ cd own-own-5097c01bcdc4

   $ sudo cp -r Eigen/ /usr/local/include/

4. Install Cufflinks .

   $ tar zxvf cufflinks-2.0.2.tar.gz

   $ cd cufflinks-2.0.2

   $ ./configure --prefix=/path/to/cufflinks/install --with-boost=/usr/local/ --with-eigen=/usr/local/include//Eigen/

   $ make

   $ make install

5. You can download the Linux x86_64 binary directly . The above tedious steps are not required, and the decompressed program can be used directly.