genomic_cotton

This repository contain the scripts generated in the project Genomic characterization of the wild-to-domesticated complex of Gossypium hirsutum in Mexico whitch is subdivided in three sections:

1. Analysis of chloroplast genomes
2. Analysis of nuclear genomes
3. Location of transgenes in the genomes

Data characteristics

• WGS
• Sequencing with Illumina NovaSeq 6000
• Library TruSeq DNA PCR free
• Paired-end

Graphic workflow by section

Prerequisites

Software to analyze the chloroplast genomes:

GetOrganelle 1.7.3.4

GeSeq

CPGAVAS2

Mauve 2.4.0

MAFFT 7.0

MEGA-X 10.2.4

SplitsTree

BEAST

Software to analyze the nuclear genome:

fastqc_v0.11.8

trim_galore 0.6.0_dev

bwa0.7.17-r1188

Samtools 1.7

Picard

NGSEP

SplitsTree

bedmap 2.4.40

R packages:

• ggplot2
• gtable
• grid
• lattice
• phyloch
• strap
• phytools
• tidyverse
• GenomicRanges

Directories

Directory organization where the letter c and n are used after the number to indicate whether the script corresponds to the chloroplast or nuclear genome analysis, respectively:

+-- genomic_cotton
|	+--bin/
|               +--1_download_seq.sh
|               +--2_quality_samples.sh
|               +--3_transgenes_blast.sh
|               +--3c_assembly_chloroplast.sh
|               +--3n_clean_data.sh
|               +--4c_mapping.sh
|               +--4n_mapping.sh
|               +--5c_sort_sequences.sh
|               +--5n_sort_sequences.sh
|               +--6c_quality_mapping.sh
|               +--6n_quality_mapping.sh
|               +--7c_find_variants.sh
|               +--7n_find_variants.sh
|               +--8c_variant_annotation.sh
|               +--8n_short_variant_annotation.sh
|               +--9_boxplot.R
|	+--data/
|               +-- transgen_db.fasta
|               +-- README_data.md
|	              +--annotation/
|                    	  +--README_annotation.md
|                         +--Predicted gene alignments_TM-1_V2.1.gene.gff.gz
|                         +--blat_AD1_transcript_ZJU_g.hirsutum_cottongen_reftransV1.p97.len97.gff3.gz
|                         +--marker_alignment_blat_AD1_ZJU_SNP.p90.len97.gaplt2.gapszlt2.gff3.gz
|                         +--other_transcript_blat_AD1_TxJGI_g.hirsutum_cottongen_refTransV1.p97.len97.gff3.gz
|                         +--predicted_gene_alignment_Tx-JGI_G.hirsutum_v1.1.gene.gff3.gz
|                         +--annotation.bed****
|	+--meta/
|               +--id_samples.txt****

/bin/

This directory contains the necessary scripts for do the structural variant analysis. Each script correspond to a step of workflow. Description each script:

• 1_download_seq.sh to download sequences of projects in NCBI
• 1.1_transgenes_blast.sh to search of transgenes sequences genomes samples
• 2_fastqc_samples.sh to do the quality analysis of sequencing with fastqc
• 3c_assembly_chloroplast.sh to do the assembly of chloroplast genomes
• 3n_clean_data.sh to clean sequences with low quality
• 4*_mapping.sh to align sequences to reference genomes
• 5*_sort_sequences.sh to convert file .sam to .bam, and to sort the aligmented genomes with Picard
• 6*_quality_mapping.sh to evaluate the quality of mapping
• 7*_find_variants.sh to identified genomic variants
• 8*_variant_annotation.sh to annotated each genomic variant
• 9_boxplot.R to generated graphics with the number of genomic variants found

/data/

Contains the description about the data obtained, and the links to the repository of data where you can found .fastq files

/meta/

Directory meta contain the additional information about the management of data

Credits

M. S. Melania Vega