Single Meiosis project:

• Bioinformatics and statistics codes to analyze the 20 tetrads of Arabidopsis thaliana from [Ref article]
• Supplementary methods, results and code to reproduce the figures.
• Final datasets

Input data:

Tetrads sequencing products are available in Biostudies: E-MTAB-14435 Each tetrad's sequencing product is made of 8 files (2 paired-end for each 4 individual).

Example:

|_tetrad:
   ├─ tetrad_M1_s1.fq
   ├─ tetrad_M1_s2.fq
   ├─ tetrad_M2_s1.fq
   ├─ tetrad_M2_s2.fq
   ├─ tetrad_M3_s1.fq
   ├─ tetrad_M3_s2.fq
   ├─ tetrad_M4_s1.fq
   ├─ tetrad_M4_s2.fq

Codes organisation:

|_bash |_R |_hmm-nco |_variantutils |_Rmd |_Data |_scripts_tetrad_processing

scripts_tetrad_processing

Contain the main scripts necessary to run tetrads analysis.

• singlemeiosis.sh (main script)
• singlemeiosis-pipeline_genotoul_V3 (conf file)
• Launch_Tetrad_Analysis_genotoul_V3.R (sub-script)

bash:

single-meiosis-pipeline

• Align tetrads on Col (TAIR10) + Ler (https://www.ncbi.nlm.nih.gov/nucleotide/LUHQ01000000) genome
• Separate bam by parental genomes (Col and Ler) and call read depth by genome position.

input:

   |_Tetrad (*.fq)
   |_Genomes
      |_ Col.fasta 
      |_ Ler.fasta 

output:

   |_Tetrad
     |_log
     |_M1
        |_ M1_Coller.bam
        |_ M1_Col.bam
        |_ M1_Ler.bam
        |_ M1_Col.vcf
        |_ M1_Ler.vcf
     |_M2
     |_M3
     |_M4
    config

R: variantutils

• Process the output of the single-meiosis bash pipeline and prepare input for hmm-nco function.
• Call the crossover.py programm.

R: hmm-nco

author: S. Robin R functions to run the HMM model.

Report

Rmd:

Supplementary methods, results and code to reproduce the figures.

Rmd/Data:

Final datasets