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mylena-s authored May 23, 2022
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Expand Up @@ -7,42 +7,15 @@ Supplementary files for Chapter 2 of my master's dissertation "Jellyfish repeato

|directory/file | description
|-------------------------------------------------------|----------------------------------------------------------
|/RepeatExplorer/ |directory including datasets resulting from RE2 pipeline
| |and the scripts used to process them and carry on
| |statistics.
| |
|/RepeatExplorer/AssemblyAnalysis.py |Python script used to manipulate files resulting from
|  |repeatmasker repeat annotation in assemblies,
|  |to identify clusters after clusterscan,
|  |and to classify them into proximal or distal to
| |gaps and ends.
| |
|/RepeatExplorer/ScyphoSat_table |table containing all information regarding satellite
| |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/Genus_ComparisonStats.py |Python script to compare satDNA features distribution in
|  |samples of the same genus.
| |
|/RepeatExplorer/SampleStatistics.py |Python script to compare satDNA features across all
|  |species and samples.
| |
|/RepeatExplorer/ |directory including datasets resulting from RE2 pipeline and the scripts used to process them and carry on statistics.
|/RepeatExplorer/AssemblyAnalysis.py |Python script used to manipulate files resulting from repeatmasker repeat annotation in assemblies, to identify clusters after clusterscan, and to classify them into proximal or distal to gaps and ends.
|/RepeatExplorer/ScyphoSat_table |table containing all information regarding satellite 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/Genus_ComparisonStats.py |Python script to compare satDNA features distribution in samples of the same genus.
|/RepeatExplorer/SampleStatistics.py |Python script to compare satDNA features across all species and samples.
|/RepeatExplorer/duplicateMonomer.py |Python script to duplicate and rename satDNA monomers.
| |
|/RepeatExplorer/filterBlastn.py |Python script to classify satDNA blast hits as variants,
|  |families and superfamilies.
| |
|/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
| |
|/dnaPipeTE/dnaPipeTE_spearmanr.R |R script used for statistical analysis between genome
|  |size and dnaPipeTE results
| |
|/dnaPipeTE/filter_RTcompleteness.py |Python script used for filtering protein domains with
|  |coverage below certain threshold
|/RepeatExplorer/filterBlastn.py |Python script to classify satDNA blast hits as variants, families and superfamilies.
|/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
|/dnaPipeTE/dnaPipeTE_spearmanr.R |R script used for statistical analysis between genome size and dnaPipeTE results
|/dnaPipeTE/filter_RTcompleteness.py |Python script used for filtering protein domains with coverage below certain threshold

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