Add structural annotations to dotplots

The example:

Recently, Franco et al. identified clusters with several similar transposable elements (belonging to the sSaTar families 1-3) within several grasses. On the sorgum chromosome 1, sSaTar transposons are arranged in a linear tandem-manner, just separated by short microsatellites. Combination of structural annotation with a dotplot, as possible with FlexiDot, allows visualisation of this peculiar region.

Franco et al. (2018) "Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes". BMC Genomics 19:271

FlexiDot illustration of this region:

Input files:

• sSaTar.fas: sSaTar cluster on Sorghum chromosome 1*
• sSaTar.gff3: sSaTar annotations as gff3*
• sSaTar.config: sSatar config file to define colors for FlexiDot

* fasta and gff3 files have been deduced from Franco et al.'s Supplemental File 14, showing the annotated sequence of this region.

The config file defines color, alpha and zoom of each sequence type. Please note, that the small microsatellite region is visualized with an additive zoom of 10.

Command:

# Set path to data in flexidot repo.
DATA="tests/test-data/sSaTar_example"

flexidot -i $DATA/sSaTar.fas -g $DATA/sSaTar.gff3 -G $DATA/sSaTar.config -k 10 -S 1 -T 30 -E 15 -A 2 -C black -f pdf

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For additional application use cases, please see the FlexiDot in-depth documentation (pdf).

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