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

Basic TIR processing

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.

If the --both flag is set, then both left and right termini will be reported with suffixes "_L_TIR" and "_R_TIR".

In this example, TIRs must be at least 10bp in length and share 80% identity and occur within 10bp of each end of the input element.

tsplit TIR -i tests/data/TIR_element.fa -d results -p TIR_split

# Equivalet to defaults
tsplit TIR -i tests/data/TIR_element.fa -d results -p TIR_split --method blastn --maxdist 10 --minid 80.0 --minterm 10 --blast_evalue 0.001 --method blastn --splitmode split

Output: results/TIR_split_tsplit_output.fasta

Report both TIRs

With --splitmode external only the outermost TIR is returned. Setting --both returns both TIRs - useful if not identical.

tsplit TIR -i tests/data/TIR_element.fa -d results -p TIR_external_both --splitmode external --both

Output: results/TIR_external_both_tsplit_output.fasta

Output PAF alignments and GFF TIR annotations

tsplit TIR -i tests/data/TIR_element.fa -d results --splitmode split --blast_evalue 0.001 --minid 60.0 --paf --gff

Output:

• results/TIR_element_tsplit_output.fasta
• results/TIR_element.gff3
• results/TIR_element.paf

Generate TIR annotated dotplot

flexidot -i tests/data/TIR_element.fa -a results/TIR_element.paf -m 2 -o results/blast_dotplot --gff results/TIR_element.gff3

Output:

tsplit LTR

Basic LTR processing

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.

If the --both flag is set, then both left and right termini will be reported with suffixes "_L_LTR" and "_R_LTR".

By default, LTRs must be at least 10bp in length and share 80% identity and occur within 10bp of each end of the input element.

tsplit LTR -i tests/data/LTR_retrotransposon.fa -d results

Output:

• results/LTR_retrotransposon_tsplit_output.fasta

Output PAF alignments and GFF LTR annotations

tsplit LTR -i tests/data/LTR_retrotransposon.fa -d results --splitmode split --blast_evalue 0.001 --minid 60.0 --paf --gff

Output:

• results/LTR_retrotransposon_tsplit_output.fasta
• results/LTR_retrotransposon.gff3
• results/LTR_retrotransposon.paf

Generate LTR annotated dotplot

flexidot -i tests/data/LTR_retrotransposon.fa -a results/LTR_retrotransposon.paf -m 2 -o results/blast_dotplot --gff results/LTR_retrotransposon.gff3