Metadata-Version: 1.0
Name: TEToolkit
Version: 1.4.11
Summary: Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions
Home-page: http://hammelllab.labsites.cshl.edu/software#TEToolkit
Author: Ying Jin, Eric Paniagua, Oliver Tam and Molly Hammell
Author-email: yjin@cshl.edu
License: GPLv3
Description: TEToolkit
        =========
        
        Version: 1.4.11
        
        TEToolkit is composed of two tools, TEpeaks and TEtranscripts, each
        described in its own section below.
        
        *NOTE* Both programs rely on specially curated GTF files, which are not
        packaged with this software due to their size. Please go to 
        `our website <http://hammelllab.labsites.cshl.edu/software#TEToolkit>`_
        for instructions to download the curated GTF files.
        
        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.
        
        
        `Github Page <https://github.com/mhammell-laboratory/tetoolkit>`_
        
        `Pypi Page <https://pypi.python.org/pypi/TEToolkit>`_
        
        `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
        
        Created by Ying Jin, Eric Paniagua, Oliver Tam & Molly Hammell, February 2014
        
        Copyright (C) 2014-2015 Ying Jin, Eric Paniagua, Oliver Tam & Molly Hammell
        Contact: Ying Jin (yjin@cshl.edu)
        
        Requirements
        ------------
        
        Python:     2.6.x or 2.7.x (not tested in Python 3.x)
        
        pysam:       0.8.2.1 or greater
        
        R:          2.15.x or greater
        
        DESeq:      1.5.x or greater
        
        
        Installation
        ------------
        
        1. Download compressed tarball.
        2. Unpack tarball.
        3. Navigate into unpacked directory.
        4. Run the following::
        
            $ python setup.py install
        
        If you want to install locally (e.g. /local/home/usr),
        run this command instead::
        
            $ python setup.py install --prefix /local/home/usr
        
        *NOTE* In the above example, you must add
        
            /local/home/usr/bin
        
        to the PATH variable, and
        
             /local/home/usr/lib/python2.X/site-packages 
        
        to the PYTHONPATH variable, where python2.X refers to the 
        python version (e.g. python2.7 if using python version 2.7.x).
        
        
        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 BED. 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
              --mode                TE counting mode. 'uniq' consider uniq-reads only. 'multi' distribute to all alignments. DEFAULT: multi
              --wig                 generate wiggle file for peaks (normalize to
                                        10 million reads in total(library size))
              -h | --help           help info
        
        
        Example Command Lines
        ----------------------
        
        ::
        
            TEpeaks --format BAM -t S1.bam --tinput S1input.bam -s mm -n sd --mode multi
        
            TEpeaks --format BAM -t S1.bam S2.bam -c C1.bam C2.bam  --tinput S1input.bam  --cinput C1input.bam -s mm -n sd --diff --mode multi
        
        
        
        TEtranscripts
        =============
        
        Usage
        -----
        
        ::
        
            usage: TEtranscripts -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:
        
              *Input/Output options*
              --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.
              --sortByPos           Input file is sorted by chromosome position.
              --project [name]      Prefix used for output files (e.g. project name)
                                    DEFAULT: TEtranscript_out
        
              *Analysis options*
              --mode [TE counting mode]
                 How to count TE:
                    uniq        (unique mappers only)
                    multi       (distribute among all alignments).
                 DEFAULT: uniq
              --minread [min_read] read count cutoff. DEFAULT: 1
              -L | --fragmentLength [fragLength]
                 Average length of fragment used for single-end sequencing
                 DEFAULT: For paired-end, estimated from the input alignment file. For single-end, ignored by default.
              -n | --norm [normalization]
                 Normalization method : DESeq_default (default normalization method of DESeq), TC (total annotated read counts), quant (quantile normalization). 
                 DEFAULT: DESeq_default
              -i | --iteration 
                 maximum number of iterations used to optimize multi-reads assignment. DEFAULT: 0
              -p | --padj [pvalue]
                 FDR cutoff for significance. DEFAULT: 0.05
              -f | --foldchange [foldchange]
                 Fold-change ratio (absolute) cutoff for differential expression. 
                 DEFAULT: 1
        
              *Other options*
              -h | --help
                 Show help message
              --verbose [number]
                 Set verbose level.
                   0: only show critical messages
                   1: show additional warning messages
                   2: show process information
                   3: show debug messages
                 DEFAULT: 2
              --version
                 Show program's version and exit
        
        *NOTE* BAM files must be either unsorted or sorted by queryname. If the BAM files are sorted by position, please use the '--sortByPos' option
        
        
        Example Command Lines
        ---------------------
        
        If BAM files are unsorted, or sorted by queryname:: 
        
            TEtranscripts --format BAM --mode multi -t RNAseq1.bam RNAseq2.bam -c CtlRNAseq1.bam CtlRNAseq.bam --project sample_nosort_test
        
        If BAM files are sorted by coordinates/position::
        
            TEtranscripts --sortByPos --format BAM --mode multi -t RNAseq1.bam RNAseq2.bam -c CtlRNAseq1.bam CtlRNAseq.bam --project sample_sorted_test
        
        
        Recommendations for TEToolkit input files
        =========================================
        
        TEToolkit can perform transposable element quantification from alignment results (e.g. BAM files) generated from a variety of programs. 
        Given the variety of experimental systems, we could not provide an optimal alignment strategy for every approach. Therefore,
        we recommend that users identify the optimal parameters for their particular genome and alignment program in order to get the best
        results.
        
        When optimizing the alignment parameters, we recommend taking these points into consideration:
        
        *Allowing sufficient number of multi-mappers during alignment*
        
        Most alignment programs provide only 1 alignment per read by default. We recommend reporting multiple alignments per read. We have found 
        that reporting a maximum of 100 alignments per read provides an optimal compromise between the size of the alignment file and recovery 
        of multi-mappers in many genome builds. However, we highly suggest that users optimize this parameter for their particular experiment, 
        as this could significantly improve the quality of transposable element quantification.
        
        *Optimizing alignment parameters for non-reference strains*
        
        It is common that the specific laboratory strains used in an experiment contains genomic variations not present in the reference strain.
        While this can be mitigated through allowing mismatches during alignments, certain lab strains (e.g. Drosophila melanogaster) have
        diverged significantly from the reference genomes. We highly recommend that users should refine their alignment procedures to better
        account for the expected variations between their lab strains and the reference genome, which will accordingly improve their analysis
        with TEToolkit. Users can also align to a custom genome build specific to their organism, though they would need GTF annotations for 
        genes and transposable elements that are compatible with their custom genome in order to utilize TEToolkit. Please contact us if you
        require advice in generating these annotation files.
        
        *Specific recommendations when using STAR*
        
        `STAR <https://github.com/alexdobin/STAR>`_ utilizes two parameters for optimal identification of multi-mappers `--outFilterMultimapNmax` and `--outAnchorMultimapNmax`. 
        The author of STAR recommends that `--outAnchorMultimapNmax` should be set at twice the value used in `--outFilterMultimapNmax`, 
        but no less than 50. In our study, we used the same number for both parameters (100), and found negligible differences in identifying 
        multi-mappers. Upon further discussion with the author of STAR, we recommend that setting the same value for `--outAnchorMultimapNmax`
        and `--outFilterMultimapNmax`, though we highly suggest users test multiple values of `--outAnchorMultimapNmax` to identify the 
        optimal value for their experiment.
        
        
        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 `this website <http://www.gnu.org/licenses/>`_.
        
        
        
Keywords: TE transposable element differential enrichment
Platform: Linux
Platform: MacOS
