# Annotation and genomes
######################

In directory data/

MAC : ptetraurelia_mac_51.fa 
MAC+IES : ptetraurelia_mac_51_with_ies.fa
MIC : ptetraurelia_mic2.fa
IES : internal_eliminated_sequence_PGM_ParTIES.pt_51.gff3 
Genes : ptetraurelia_mac_51_annotation_v2.0.gff3 
TE : ptetraurelia_mic2_TE_annotation_v1.0.gff3
available on ParameciumDB (https://paramecium.i2bc.paris-saclay.fr/download/Paramecium/tetraurelia/51/)
ref Arnaiz et al. 2012, 2017 Guérin et al. 2017

# Software and scripts
####################
ParTIES (v1.05) https://github.com/oarnaiz/ParTIES (Denby Wilkes et al.)
Bowtie2 (v2.2.9) (--local -X 500 paired-end mode)
R (v4) packages : ComplexHeatmap (v2.6.2); GenomicRanges (v1.42), ggplot2 (v3.3.5)


# Cell stages (support Fig1)
####################
In directory StageKineticPgmL1

# Basic sequencing & mapping stats
####################
In directory SequencingStats

# Check old MAC fragments contamination
####################
In directory Contamination

# Calculation of the ploidy
####################
In directory PloidyEstimation

# Various analysis using the IES excision scores
####################
In directory IES_Excision_Score

# Coverage of the MIC genome
####################
In directory MIC_coverage

# Coverage of annotated Transposable Elements compared to IESs
####################
In directory TE_vs_IES_coverage

# Detection of telomere addition sites
####################
In directory Telomeres

# Detection of excised IES junctions (IES-IES junctions)
####################
In directory IES-IES_junctions

# SeqLogo analyses using different IES datasets
####################
In directory SeqLogo

# Detection of rare IES excision errors (accuracy)
####################
In directory Excision_Errors


# Annotation of new IES within MIC-limited regions
####################
In directory IES_MIC-limited







