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TEToolkit 1.2.1e

Tools for estimating differential enrichment of Transposable Elements or other highly repetetive regions

Latest Version: 1.4.11

TEToolkit
=========

Created by Ying Jin, Oliver Tam, and Molly Hammell at CSHL, February 2014

Copyright (C) 2014 Ying Jin, Oliver Tam, and Molly Hammell
Contact: Ying Jin (yjin@cshl.edu)


Summary
-------

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 check back for an
update to this package's homepage. Once it is up and running, the required
GTFs will be downloadable from there.

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


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=""/>.


================================
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: 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.
-i | --iteration
maximum number of iterations used to optimize multi-reads assignment. DEFAULT: 0


Example Command Lines
---------------------

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

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  
File Type Py Version Uploaded on Size
TEToolkit-1.2.1e.tar.gz (md5) Source 2014-05-30 73KB
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