Description

Tiglon is a genome-guided transcriptome assembler that is specifically designed to integrate alignments of different mapping tools(such as Hisat2 and Star) to build the labeled splice graph and to extract more reliable paired paths. Tiglon employs a dynamic programming algorithm to recover the transcripts by making strategic use of the label-information. The software has been developed to be user-friendly, which is available at https://github.com/yutingsdu/Tiglon-v.1.1.git.

The software takes a file that lists alignment files generated by different aligners as input, and outputs all assembled candidate transcripts in GTF format.

This software is free to use, modify, redistribute without any restrictions, except including the license provided with the distribution.

** Note **

The current version of Tiglon can accepts BAM files generated by Hisat(2) and Star.

Installation

Prerequisites

g++ with support for C++11 (e.g. 4.7.2)

Boost >= 1.47.0

Bamtools (now tested with 2.5.2 -- the makefile also contains instructions for older versions)

libz

1. Installing Boost

a) download a version of boost and unpack it

    $ tar zxvf boost_1_47_0.tar.gz

b) change to the boost directory and run ./bootstrap.sh

    $ cd boost_1_47_0
    $ ./bootstrap.sh

c) run

    $ ./b2 install --prefix=/your/boost/dir

    ########################################################################
    #  
    #  For example, 
    #
    #  if you want to install boost in /home/yuting/local/boost, the command is :
    #
    #  $ ./b2 install --prefix=/home/yuting/local/boost
    #
    #  If the boost is installed successfully, you would find two sub-directories:
    #
    #  /home/yuting/local/boost/include/
    #  /home/yuting/local/boost/lib/
    #
    #########################################################################

Note: The default Boost installation directory is /usr/local. Take note of the boost 
installation directory, because you need to tell the Tiglon installer where to find 
boost later on.

2. Installing BamTools

Download bamtools via: git clone https://github.com/pezmaster31/bamtools.git

Build bamtools by following the steps below.

a) go to the bamtools directory and make a new directory named "build"

    $ mkdir build
    $ cd build

b) type cmake and make it install

    $ cmake -DCMAKE_INSTALL_PREFIX=/your/bamtools/dir ..
    $ make
    $ make install

    where CMAKE_INSTALL_PREFIX is the root of your final installation directory.

    ##########################################################################
    #  
    # For example,
    # 
    # if you want to install bamtools in /home/yuting/local/bamtools, the command is :
    # 
    # $ cmake -DCMAKE_INSTALL_PREFIX=/home/yuting/local/bamtools ..
    # $ make
    # $ make install
    #    
    # If the bamtools is installed successfully, you would find two sub-directories:
    #
    # /home/yuting/local/bamtools/include
    # /home/yuting/local/bamtools/lib64
    #
    ##########################################################################

As an altanitive, you can build bamtools based on the instruction at
https://github.com/pezmaster31/bamtools/wiki/Building-and-installing

Note: you need to tell the Tiglon installer where to find bamtools later on.

3. Building Tiglon

Change to the Tiglon-v.1.1/src directory and make

    $ cd src
    $ make all release BOOST_PATH=/your/boost/dir BAMTOOLS_PATH=/your/bamtools/dir

    where BOOST_PATH is the aformentioned directory where you installed the boost 
    and BAMTOOLS_PATH is the directory where you installed the bamtools.

    #########################################################################
    #
    # For example,
    #
    # if you installed boost in /home/yuting/local/boost and 
    # installe bamtools in /home/yuting/local/bamtools, the command is :
    #
    # $ make all BOOST_PATH=/home/yuting/local/boost BAMTOOLS_PATH=/home/yuting/local/bamtools
    #
    ##########################################################################

If the Tiglon is installed successfully, you'll see the following 5 executable files in Tiglon-v.1.1/src/bin/
tiglon_abundance, tiglon_cover, tiglon_graph, tiglon_merge, tiglon_path_search.

4. Running Tiglon

a) Type the following command OR Set the LD_LIBRARY_PATH enviroment variable

    $ export LD_LIBRARY_PATH=/home/yuting/local/boost/lib:$LD_LIBRARY_PATH

    Note: please replace "/home/yuting/local/boost/lib" with your own directory "/your/boost/dir/lib"

    ##########################################################################
    #           !!!!!!!!!! PLEASE NOTE !!!!!!!!!!
    #
    #  If you do not set this variable , you would possible see the follwoing error information:
    #
    # "error while loading shared libraries: libboost_serialization.so.1.47.0:
    #                  cannot open shared object file: No such file or directory"
    #
    ##########################################################################

b) The executable Tiglon is in the Tiglon-v.1.1 directory

    $ Tiglon -B bamFile_list -s first -o Tiglon_outdir

    where the bamFile_list is a file that lists the alignments BAM files (one per line).

5. Testing Tiglon on a demo data set:

To test if you have succesfully installed Tiglon, please download the demo data set from

https://sourceforge.net/projects/tiglon/files/DemoData/.

At this website you will see two alignments files produced by Hisat2 and Star (Hisat.bam and Star.bam)

Put the Hisat.bam and Star.bam in the directory Tiglon-v.1.1/sample_test/ and change to Tiglon-v.1.1/sample_test/

Type the following command:

    $ ./run_me.sh

If you get the tiglon_outdir/Tiglon.gtf, congratulations, you have succesfully installed the Tiglon.

===========================================================================

Tiglon v.1.1 usage:

** Required **

--bam/-B <string>: path to the file listing the alignments BAM files (one per line)

--strand/-s <string>: Strand-specific RNA-Seq reads orientation.

 If reads are paired:
  1) Use <unstranded> to indicate RNA-seq reads are non-strand-specific.
  2) Use <first> to indicate fr-first-stranded RNA-seq reads.
  3) Use <second> to indicate fr-second-stranded RNA-seq reads.

 If reads are single:
  1) Use <single_unstranded> to indicate RNA-seq reads are non-strand-specific.
  2) Use <single_forward> to indicate RNA-seq reads are forward.
  3) Use <single_reverse> to indicate RNA-seq reads are reverse.

---

** Options **

--help/-h           : Output Tiglon Help Information

--version/-v            : Print current version of Tiglon

--output_dir/-o <string>    : Output path, default: tiglon_outdir

--min_trans_cov/-c <float>  : Minimum expression level estimated by abundance analysis for output, default: >0.

--min_trans_length/-L <int>     : Minimum assembled transcript length, default: 500.

--min_average_frac/-d <float>   : Minimum junction coverage fraction by average junction coverage, default: 0.03.

--min_unbalance_frac/-D <float> : Minimum fraction of unbalanced junction, default: 0.03.

--min_gap_length/-e <int>       : Minimum gap length between two exons, default: 200.

--thread/-p <int>       : Number of threads to use (default: 2)

---

** Typical commands **

(i) A typical Tiglon command for paired-end data might be:

  Tiglon -B bamFiles_list -s first -o Tiglon_outdir -p 2

(ii) A typical Tiglon command for single-end data might be:

  Tiglon -B bamFiles_list -s single_reverse -o Tiglon_outdir -p 2

===========================================================================

Authors: Ting Yu designed and wrote Tiglon.

Contact: Any questions, problems, bugs are welcome and should be dumped to Ting Yu yutingsdu@163.com Created on Oct 6, 2021.