TEToolkit protocols

TEToolkit specifications

Information


Unique identifier OMICS_09465
Name TEToolkit
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Alignment files in either the SAM or BAM format and two annotation files in the General Transfer Format (GTF) for genes and TEs respectively.
Input format BAM,SAM,GTF
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements pysam, R, DESeq
Maintained Yes

Subtools


  • TEpeaks
  • TEtranscripts

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Maintainer


  • person_outline Molly Hammell <>

Publication for TEToolkit

TEToolkit IN pipelines

 (3)
2017
PMCID: 5607212
PMID: 28854222
DOI: 10.1371/journal.pgen.1006964

[…] using star version 2.4.0f1 [83] to the mouse genome (grcm38/mm10) using gencode m11 transcriptome assembly [84] for junction points. coding genes and transposable elements were quantified using tetoolkit [85] to annotate both uniquely and ambiguously mapped reads. gencode annotation and repbase database [86] for repetitive sequences and transposable elements were used […]

2017
PMCID: 5703239
PMID: 28524723
DOI: 10.1080/19491034.2017.1330238

[…] tetranscript64 to obtain read count tables for transcripts and transposons, using the te annotation as provided by the authors of tetranscript (http://labshare.cshl.edu/shares/mhammelllab/www-data/tetoolkit/te_gtf/mm10_rmsk_te.gtf.gz). normalization and differential expression analysis was done using deseq2.65, q-pcr was performed on a steponeplus real-time pcr system (applied biosystems) […]

2016
PMCID: 5389475
PMID: 27923996
DOI: 10.1093/nar/gkw1197

[…] (56) to obtain read count tables for transcripts and transposons, using the te annotation as provided by the authors of tetranscript (http://labshare.cshl.edu/shares/mhammelllab/www-data/tetoolkit/te_gtf/mm10rmskt e.gtf.gz). normalization and differential expression analysis was done using deseq2 (57)., for figures 1a and 3a, tet1cdmut + gfp and mock were excluded from statistical […]

TEToolkit institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
TEToolkit funding source(s)
Supported by the Rita Allen Foundation and by a grant from the National Science Foundation [MCB-1159098] and by a CSHL Cancer Center Support Grant from the National Institutes of Health (NIHNCI-CA-045508).

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