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TEToolkit 0.9

(FAILED UPLOAD) Tools for estimating differential enrichment of Transposable Elements or other highly repetetive regions.

Latest Version: 1.0

TEToolkit
=========

Created by Ying Jin, Eric Paniagua & Oliver Tam, February 2014

Copyright (C) 2014 Ying Jin, Eric Paniagua & Oliver Tam
Contact: Ying Jin (yjin@cshl.edu)


Summary
-------

    TEToolkit is composed of two tools, TEpeaks and TEtranscripts, each described in
    its own section below.

    TEpeak takes ChIP-seq (and similar data) alignment files (BAM or BED),
    identiifes narrow peaks, and is also able to do differential analysis over
    peaks of two sets of libraries. It is an extension of MACS by adding the
    funcionality of taking into account multi-reads, another normalization
    method, bin correlation, and differential analysis. The differential
    analysis is performed using DESeq.

    TEtranscripts takes RNA-seq (and similar data) and annotates reads to both
    genes & transposable elements. It then performs differential analysis using
    DESeq.


Requirements
------------

    Python:     2.6.x or 2.7.x (not tested in Python 3.x)
    Samtools    (tested using version 0.1.19)
    HTSeq       (tested using version 0.5.4p3)
    R:          2.15.x or greater
    DESeq:      1.5.x or greater


================================
TEpeaks
================================

Usage
-----
usage: TEpeaks -t treatment sample [treatment sample ...]
                    -c control sample [control sample ...]
                    --tinput treatment input
                    --cinput control input
                    -s genome
                    [optional arguments]

Required arguments:
  -t | --treatment [treatment sample 1 treatment sample 2...]
     Sample files in group 1 (e.g. treatment/mutant), separated by space
     Sample files in group 2 (e.g. control/wildtype), separated by space
  --tinput    treatment input
  -s genome  (hg: human19, mm: mouse9, dm: dm3)

Optional arguments:
  -c | --control [control sample 1 control sample 2 ...]
  --cinput  control input
  --format [input file format]
     Input file format: BAM or SAM. DEFAULT: BAM
  --project [name]      Name of this project. DEFAULT: TEpeak_out
  -p | --padj [pvalue]
     FDR cutoff for significance. DEFAULT: 1e-5
  -n | --norm [normalization]
     Normalization method : sd (library size),
                            bc (bin correlation). DEFAULT: sd
  -r | --step           step size. DEFAULT: 100
  -a | --auto           auto detect shiftsize. DEFAULT: False
  -d | --diff           require differential analysis
  -g | --gap            maximum allowed gap. DEFAULT: 1000
  -f | --fragsize       fragment size. DEFAULT: 200
  --lmfold              lower bound of fold change for modeling shipsize.
                        DEFAULT: 10
  --umfold              upper bound of fold change for modeling shiftsize.
                        DEFAULT: 30
  --minread             minimal reads of a peak. DEFAULT: 5
  --wig                 generate wiggle file for peaks (normalize to
                            10 million reads in total(library size))
  -h | --help           help info


Testing TEpeaks
---------------

All files are found in the "data/test/TEpeaks" folder of the source
distribution.

Command line
............

TEpeaks --format BAM -t S1.bam --tinput S1input.bam -s mm -n sd

TEpeaks --format BAM -t S1.bam S2.bam -c C1.bam C2.bam  --tinput S1input.bam  --cinput C1input.bam -s mm -n sd --diff



================================
TEtranscripts
================================

Usage
-----
usage: TEtranscript -t treatment sample [treatment sample ...]
                    -c control sample [control sample ...]
                    --GTF genic-GTF-file
                    --TE TE-GTF-file
                    [optional arguments]

Required arguments:
  -t | --treatment [treatment sample 1 treatment sample 2...]
     Sample files in group 1 (e.g. treatment/mutant), separated by space
  -c | --control [control sample 1 control sample 2 ...]
     Sample files in group 2 (e.g. control/wildtype), separated by space
  --GTF genic-GTF-file  GTF file for gene annotations
  --TE TE-GTF-file      GTF file for transposable element annotations

Optional arguments:
  --format [input file format]
     Input file format: BAM or SAM. DEFAULT: BAM
  --stranded [option]   Is this a stranded library? (yes, no, or reverse).
                        DEFAULT: yes.
  --mode [TE counting mode]
     How to count TE:
        uniq        (unique mappers only)
        sameFam     (group TE by family)
        sameInst    (assign to dominant TE)
        multi       (distribute among all alignments).
     DEFAULT: uniq
  --project [name]      Name of this project. DEFAULT: TEtranscript_out
  -p | --padj [pvalue]
     FDR cutoff for significance. DEFAULT: 0.05
  -f | --foldchange [foldchange]
     Fold-change ratio (absolute) cutoff for differential expression.
     DEFAULT: 1
  -n | --norm [normalization]
     Normalization method : rpm (reads per million mapped),
                            quant (quantile normalization). DEFAULT: rpm
  --no-sort             Input file is not sorted by chromosome position.

Example:
TEtranscripts --format BAM --mode uniq -t RNAseq1.bam RNAseq2.bam -c CtlRNAseq1.bam CtlRNAseq.bam


Testing TEtranscripts
---------------------

All files are found in the "data/test/TEtranscript" folder of the source
distribution.

Input BAM files:    sample1.bam
                    sample2.bam
Gene GTF file:      sample_refgene.gtf  (mm9 refgene)
TE GTF file:        sample_rmsk.gtf     (mm9 rmsk)


Command line
............

TEtranscripts -t sample1.bam -c sample2.bam --format BAM --GTF sample_refgene.gtf --TE sample_rmsk.gtf --norm rpm --mode sameFam --project sample_test_rpm

Expected output in "test/output" folder.


Copying & distribution
----------------------

    TEtranscripts and TEpeaks are part of TEToolKit.

    TEToolKit is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with TEToolKit.  If not, see <http://www.gnu.org/licenses/>.
 
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