AthalianaTETranscripts

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AthalianaTETranscripts

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Arabidopsis thaliana TE transcript-based annotation added on top of TAIR10 annotation

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# Arabidopsis thaliana TE Transcripts
TE transcript-based annotation layered over Arabidopsis TAIR10 TE annotation\
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TAIR10 TE annotation provides 6 columns of information for each Transposable Element (TE): TE-ID, If the orientation is 5’, TE Start, TE End, TE Family and TE superfamily/Type\
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This information is available in the first 9 columns of the new annotation bed file.\
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A typical bed file format is followed where the first 6 columns are: Chromosome, Start, Stop, TE-ID, Score, Strand. This format is chosen for ease of data analysis using BEDTools.\
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In addition, the following columns are noted for each TE:\
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7: Subfamily of the TE.\
8: Family of the TE.\
9: Super Family of the TE.\
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10: Length of the TE.\
11: Length Category of the TE as described in Panda et. al., Genome Biology 2016.\
12: Copy# of the TE subfamily.\
13: Copy# category of the TE subfamily as described in Panda et. al., Genome Biology 2016.\
14: Distance from the centromere.\
15: Position category based on distance from centromere as described in Panda et. al., Genome Biology 2016.\
16: Distance from the nearest gene.\
17: Type of RNA-directed DNA methylation (RdDM) acting on the TE when TEs are silent (wt Col) as reported in Panda et. al., Genome Biology 2016.\
18: Type of RdDM acting on the TE when TEs are active (*ddm1*) as reported in Panda et. al., Genome Biology 2016.\
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19: Evidence of Expression:\
	“.” if no expression found\
	“**Low Expressed**” if at least 1 read reported expression but not enough to annotate transcripts\
	“**ExpressedAndAnnotated**” if TE is expressed high enough for transcript annotation.\
20: Transcriptional Start Site (TSS). Comma separated values note multiple TSSs.\
21: Transcriptional Stop Site or more accurately polyadenylation site.\
22: Transcriptional Strand. Comma separated valued not direction of each transcript.\
23: Transcript ID. This transcript ID can be cross-referenced in the GFF file for investigating exon intron structure.\
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References\
Panda, K., Ji, L., Neumann, D. A., Daron, J., Schmitz, R. J., & Slotkin, R. K. (2016). Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology, 17(1), 170. http://doi.org/10.1186/s13059-016-1032-y

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