CLI Tutorial
Overview
The tsplit command is used to split transposable elements into their internal and external segments. It can be used for both long terminal repeats (LTRs) and terminal inverted repeats (TIRs).
The command line tools use sequence alignment to identify the boundaries of the segments based on user-defined parameters.
Example usage
tSplit can be run in two modes: tsplit LTR and tsplit TIR, for extracting long terminal repeats or terminal inverted repeats, respectively.
Options are the same for each.
tsplit TIR
For each element in TIR_element.fa split into internal and external (TIR) segments.
Split segments will be written to TIR_split_tsplit_output.fasta with suffix "_I" for internal or "_TIR" for external segments.
TIRs must be at least 10bp in length and share 80% identity and occur within 10bp of each end of the input element.
Additionally, synthetic MITEs will be constructed by concatenation of left and right TIRs, with internal segments excised.
tsplit TIR -i tests/data/TIR_element.fa -p TIR_split --makemites --keeptemp
# Equivalet to defaults
tsplit TIR -i tests/data/TIR_element.fa -p TIR_split --maxdist 10 --minid 80.0 --minterm 10 --method blastn --splitmode split --makemites --keeptemp
Output: TIR_split_tsplit_output.fasta
tsplit LTR
For each element in LTR_retrotransposon.fa split into internal and external segments.
Split segments will be written to LTR_split_tsplit_output.fasta with suffix "_I" for internal or "_LTR" for external segments.
LTRs must be at least 10bp in length and share 80% identity and occur within 10bp of each end of the input element.
Output: LTR_split_tsplit_output.fasta