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@mylena-s
mylena-s authored May 23, 2022
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Supplementary files for Chapter 2 of my master's dissertation "Jellyfish repeatomes uncover hidden satellite diversity and provide insights into the C-value enigma"


The files and directories included in this folder include the following:
The files and directories included in this folder correspond to "Supplementary file S1" of the dissertation
and include the following:

directory/file description

# directory/file description

/RepeatExplorer/ directory including datasets resulting from RE2 pipeline
/RepeatExplorer/ directory including datasets resulting from RE2 pipeline
and the scripts used to process them and carry on
statistics.

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gaps and ends.

/RepeatExplorer/ScyphoSat_table table containing all information regarding satellite
monomers obtained with RE2, including manual curation
  information, classification and sequence information.
monomers obtained with RE2, including manual curation
  information, classification and sequence information.

/RepeatExplorer/assemblySat_plots.py Python script to plot the distribution of intragenomic
divergence of satellites in assemblies and reads.
/RepeatExplorer/assemblySat_plots.py Python script to plot the distribution of intragenomic
divergence of satellites in assemblies and reads.

/RepeatExplorer/Genus_ComparisonStats.py Python script to compare satDNA features distribution in
  samples of the same genus.
Expand All @@ -35,11 +35,11 @@ Supplementary files for Chapter 2 of my master's dissertation "Jellyfish repeato
/RepeatExplorer/filterBlastn.py Python script to classify satDNA blast hits as variants,
  families and superfamilies.

/dnaPipeTE/ directory including datasets resulting from dnaPipeTE and
/dnaPipeTE/ directory including datasets resulting from dnaPipeTE and
the scripts used to process them and carry on statistics

/dnaPipeTE/SupplementaryTableS2extended general repetitive content information including
detailed abundance information about all TE Superfamilies
detailed abundance information about all TE Superfamilies

/dnaPipeTE/dnaPipeTE_spearmanr.R R script used for statistical analysis between genome
  size and dnaPipeTE results
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