TEToolkit protocols

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TEToolkit specifications


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
pysam, R, DESeq
Maintained Yes


  • TEpeaks
  • TEtranscripts



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  • person_outline Molly Hammell <>

Publication for TEToolkit

TEToolkit in pipelines

PMCID: 5607212
PMID: 28854222
DOI: 10.1371/journal.pgen.1006964

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

PMCID: 5703239
PMID: 28524723
DOI: 10.1080/19491034.2017.1330238

[…] tetranscript 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., q-pcr was performed on a steponeplus real-time pcr system (applied biosystems) […]

PMCID: 5110550
PMID: 27900322
DOI: 10.3389/fmolb.2016.00076

[…] refseq gene annotations (pruitt et al., ). te expression levels—for alu, l1 and sva elements—were quantified using reads mapped to repeatmasker annotations, which were subsequently analyzed with the tetranscripts package (jin et al., ). the tetranscripts program uses an expectation maximization (em) algorithm to choose optimal unique te locations for multi-mapped reads, thereby allowing […]

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

[…] tetranscript () 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 ()., for figures and , tet1cdmut + gfp and mock were excluded from statistical tests […]

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TEToolkit in publications

PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] these tools include melt, retroseq, epiteome and mcclintock for te insertion site identification [–], t-lex to identify presence/absence of te copies [], clari-te to resolve nested te structure [], tetoolkit/tetranscripts for te enrichment analysis from experiments such as rna-seq and chip-seq [, ], and many others. which tool to use is specific to the desired type of analysis and biological […]

PMCID: 5654764
PMID: 29066820
DOI: 10.1038/s41467-017-01195-y

[…] correlation to 6ma dynamic changes since stress could result in subtle changes in expression. gene ontology analyses were performed by gene ontology consortium. transposon expression was analyzed by tetranscripts. circos plot was generated by r-package goplot. the global spearman correlations between 6ma and 5mc were performed by deeptools., cortex-specific enhancer and cortex general enhancers […]

PMCID: 5354250
PMID: 28301478
DOI: 10.1371/journal.pgen.1006635

[…] reads mapped to ribosomal rnas were removed from each library. for the remaining reads, expression abundance estimation and differential expression analysis were performed using the tetranscripts package []. reads for each library were normalized based on library size, e.g., reads per million mapped (rpm). statistically significant differences were taken […]

PMCID: 5324221
PMID: 28231763
DOI: 10.1186/s12864-017-3566-0

[…] is de-methylated and transposons are actively transcribed. previous studies have shown that their expression patterns are dynamic and stage-specific [, , , ]. to estimate their abundance, we used tetranscripts software [] with a special index file derived from repeatmasker data available at ucsc genome browser website []. additional file : figure s6 shows the expression pattern […]

PMCID: 5319189
PMID: 28219335
DOI: 10.1186/s12870-017-0996-4

[…] for multiple testing adjustment of p-values., for te family expression analysis, reads were aligned using the star 2-pass method [] allowing up to 100 multi-mapped locations (per recommendation of tetranscripts). quantification and testing for differential expression of tes were performed using tetranscripts [] with the developer-provided arabidopsis te family annotation., rna samples of msh1 […]

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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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