*** INSEGT - INtersecting SEcond Generation sequencing daTa with annotation ***

---------------------------------------------------------------------------
Table of Contents
---------------------------------------------------------------------------
  1.   Overview
  2.   Installation
  3.   Usage
  4.   Input Format
  5.   Output Format
  6.   Contact

---------------------------------------------------------------------------
1. Overview
---------------------------------------------------------------------------

INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or 
paired-end) by using gene annotations.
It can measure exon, transcript and gene expression levels of given 
annotations. If read alignments span more than one exon, INSEGT can also 
compute possible exon combinations (tuple) and their expression levels.
According to requirements it computes maximal tuple or tuple with a certain 
length. For paired-end reads INSEGT builds also tuple, whose exons are 
connected by matepairs.
Briefly it searches the intervals of the read alignments in the intervals 
of the given annotations. It counts the mapped reads for each annotation and 
its parent annotation and stores the mapped annotations for each read.
INSEGT produces three output files:
The first contains the expression levels of the given annotations.
The second contains for each given read the mapped annotations.
If the read mapped in not annotated regions, an UNKNOWN_REGION in the output will mark
this.
And the third file contains exon tuple and their expression levels.  
(For further informations see: 
http://www.inf.fu-berlin.de/en/groups/abi/theses/bachelor/finished/krakau/bsc_thesis_krakau.pdf)

---------------------------------------------------------------------------
2. Installation
---------------------------------------------------------------------------

INSEGT is distributed with SeqAn - The C++ Sequence Analysis Library (see 
http://www.seqan.de). To build INSEGT do the following:

Follow the "Getting Started" section on http://trac.seqan.de/wiki and check
out the latest SVN trunk. Instead of creating a project file in Debug mode,
switch to Release mode (-DCMAKE_BUILD_TYPE=Release) and compile insegt. This
can be done as follows:

  svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk
  mkdir seqan-trunk-build
  mkdir seqan-trunk-build/release
  cd seqan-trunk-build/release
  cmake ../../seqan-trunk -DCMAKE_BUILD_TYPE=Release
  make insegt


---------------------------------------------------------------------------
3. Usage
---------------------------------------------------------------------------

Usage: insegt [OPTIONS] <ALIGNMENTS-FILE> <ANNOTATIONS-FILE> 

INSEGT expects at least two files:
A SAM file which contains the alignments of the reads and a GFF file which 
contains the gene annotations (annotations can be also given in the
GTF format, but this has would have to be specified additionally with the 
option -z).
Without any additional parameters INSEGT would compute all tuple up to the 
length 2. That means that it builds only 2-tuple, whose exons are connected 
by matepairs.  
The default behaviour can be modified by adding the following options to 
the command line:

---------------------------------------------------------------------------
3.1. Options
---------------------------------------------------------------------------

  [ -p PATH ],  [ --output-path TEXT ]

  Path to the directory, where the output files should be stored. 
  The default value is the insegt directory.

  [ -n NUM ],  [ --ntuple INT ]

  Tuple length parameter. By default it is 2.	

  [ -o NUM ],  [ --offset-interval INT ]

  The offset-parameter to short alignment intervals to search them in the
  given annotation regions. The default value is 5.

  [ -t NUM ],  [ --threshold-gaps INT ]

  The number of gaps, which are allowed in the read alignments, for which 
  the gaps are not interpreted as introns. The default value is 5.

  [ -c NUM ],  [ --threshold-count INT ]

  Threshold for min. count of tuple, for which the tuple are given out.
  The default value is 1. 
  
  [ -r NUM ],  [ --threshold-rpkm DOUBLE ]
  
  Threshold for min. RPKM-value of tuple, for which the tuple are given out.
  The default value is 0.0.
  
  [ -m],  [ --max-tuple ]

  Only maximal tuple are computed, which are spanned by the whole read. 

  [ -e ],  [ --exact-ntuple ]
  
  Only tuple of the given length are computed. By default all tuple up to 
  the given length are computed. (If -m is set, -e will be ignored) 
  
  [ -u ],  [ --unknown-orientation ]
  
  Read-orientations are unknown. The alignment intervals are searched in the 
  annotations of both strands. By default they're just searched in the 
  annotations corresponding to the given orientation of the read.

  [ -f],   [ --fusion-genes ]

  Check for fusion genes. A separate output for matepair tupel, which map in 
  different genes, is created. By default there is no check for fusion genes.

  [ -z],   [ --gtf-format ]

  The gene annotations are given in a GTF file (instead of GFF).
  By default INSEGT expects a GFF file.

---------------------------------------------------------------------------
4. Input General Feature Format
---------------------------------------------------------------------------

INSEGT expects a GFF file which contains the gene annotations.

The General Feature Format (GFF) is specified by the Sanger Institute as a tab-
delimited text format with the following columns:

<seqname> <src> <feat> <start> <end> <score> <strand> <frame> [attr] [cmts]

See also: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

INSEGT requires additional specifications for the input of the exon- and genenames.

Input columns:
(Irrelevant fields are represented as "<>", their contents doesn't matter)

<Sequenzname> < > < > <Start> <Ende> < > <Strang> < > <ID;ParentID> 

Example:

 chr1          .   .   200     1000   .   +        .   ID=ENSG1
 chr1          .   .   300     450    .   +        .   ID=ENSG1-1;ParentID=ENSG1
 chr1          .   .   700     600    .   -        .   ID=ENSG2-1;ParentID=ENSG2

The order of the row-entries doesn't matter.
If no entry exists for the parent of an exon, INSEGT generates it automatically.
Moreover parent entries don't need start- and end-positions.


---------------------------------------------------------------------------
5. Output Formats
---------------------------------------------------------------------------

INSEGT output files are GFF files. The first output file contains the annotations 
similar to the GFF input and additionally the counts of the mapped 
reads and the normalized expression levels in RPKM (reads per kilobase of 
exon model per million mapped reads).
The two other output files have different specifications.


---------------------------------------------------------------------------
5.1. Output for annotations (annoOutput.gff):
---------------------------------------------------------------------------

Output columns:

<sequencename> < > < > <start> <end> <count> <strand> < > \
    <ID=annotationname;[ParentID=parentname;]expression-level (RPKM)> 

Example:

 chr1           .   .   30      .     60      +        .   ID=P1;30.0;
 chr1           .   .   75      300   20      +        .   ID=E1;ParentID=P1;25.0;  
 

---------------------------------------------------------------------------
5.2. Output for reads (readOutput.gff):
---------------------------------------------------------------------------

The read-output of INSEGT contains the mapped annotations followed by their 
parent annotation. If the read mapped in annotations of different parents,
the annotations are presented one after another corresponding to their parents.
Consecutive mapped annotations are separated by ":".
Overlapping annotations which are mapped by the same read interval are separated by ";". 

Output columns:

<readname> <sequencename> <strand> <annotationnames> <parentname1> \
   [<annotationnames>   <parentname2> ...]

Example:

 read_1     chr1           +        E1:E2-1;E2-2:E3   P1            E10:UNKNOWN_REGION  P2   


---------------------------------------------------------------------------
5.3. Output for tuple (tupleOutput.gff):
---------------------------------------------------------------------------

In the tuple-output of INSEGT exons which are connected by a single read are 
separated by ":" and exons which are connected by a matepair are separated by "^".

Output columns:

<sequencename> <parentname> <strand> <tupel of annotationnames> <count> <expression-level (RPKM)>


Example:

 chr1           P1           +        E1:E2-1:E3^E7              50      30.0
 chr1           P1           +        E1:E2-2:E3^E7              10      11.32


---------------------------------------------------------------------------
6. Example
---------------------------------------------------------------------------

There are small example files in the folder 
seqan-trunk/extras/apps/insegt/example/ containing alignments and 
annotations. In the following you can see how to use INSEGT with default 
paramters to analyze the alignments of the reads using the given annotations:

 1) ./extras/apps/insegt/insegt \
        ../../seqan-trunk/extras/apps/insegt/example/alignments.sam \
        ../../seqan-trunk/extras/apps/insegt/example/annotations.gff 

This computes all tuple up to the length 2 and outputs them. To only output 
tuple with a min. count of 2 you can use the option -c:

 2) ./extras/apps/insegt/insegt -c 2 \
        ../../seqan-trunk/extras/apps/insegt/example/alignments.sam \
        ../../seqan-trunk/extras/apps/insegt/example/annotations.gff 


---------------------------------------------------------------------------
7. Contact
---------------------------------------------------------------------------

For questions or comments, contact:
  David Weese <weese@inf.fu-berlin.de>
  Marcel H. Schulz <marcel.schulz@molgen.mpg.de>
  Sabrina Krakau <krakau@mi.fu-berlin.de>
