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Gene duplication analysis in B. lanceolatum new reference genome (BraLan3)

Folder structure:

  • Data: Raw data
  • Metadata: Metadata files
  • Scripts: Scripts to process data (detailed below)
  • Results: Results of the processement of the Data by Scripts
  • ScriptsPlots: Scripts generating plots/tables
  • Plots: Generated from ScriptsPlots
  • tmp: err and out files & temporary files

Assembly statistics

Extract basic assembly quality statistics from assemblies:

  • Branchiostoma_lanceolatum.BraLan3
  • Branchiostoma_lanceolatum.BraLan2
  • Branchiostoma_belcheri.Haploidv18h27
  • Branchiostoma_floridae.Bfl_VNyyK
  • Danio_rerio.GRCz11
  • Gallus_gallus.GRCg6a
  • Homo_sapiens.GRCh38
  • Mus_musculus.GRCm39
Scripts:
  • Scripts/AssemblyStatistics/ExtractAssemblyStatistics.sh

Extracts basic statistics per assembly

  • Scripts/AssemblyStatistics/Run_ExtractAssemblyStatistics.sh

Runs te above script for all assemblies and joins the results

Usage:
sbatch -t 01:00:00 --mem=8000 -J AssemblyStatistics -o tmp/AssemblyStatistics.out -e tmp/AssemblyStatistics.err Scripts/AssemblyStatistics/Run_ExtractAssemblyStatistics.sh

Gene expression

Gene expression analysis of Marletaz et al. 2018 RNA seq data

Download SRA data

Scripts:
  • Scripts/DownloadSRAData/DownloadSRAData.sh
  • Scripts/DownloadSRAData/DownloadSRAData_perSample.sh
  • Scripts/DownloadSRAData/SRA_to_fastq_perSample.sh
Usage:
./Scripts/DownloadSRAData/DownloadSRAData.sh Data/RNA-seq/Marletaz2018 <(cat Metadata/Marletaz2018_RNAseq_SRA.list)

Gene expression analysis

Scripts:

Prepare GTF and kallisto index

  • Scripts/GeneExpression/PrepareFiles.sh

Run FASTQC and kallisto per sample

  • Scripts/GeneExpression/Geneexpression_fastqc_kallisto.sh
  • Scripts/GeneExpression/FASTQC_PerSample.sh
  • Scripts/GeneExpression/Kallisto_PerSample.sh

Join results by gene with Tximport

  • Scripts/GeneExpression/JoinResultsByGene_Tximport.sh
  • Scripts/GeneExpression/JoinResultsByGene_Tximport.R
Usage:
sbatch -t 01:00:00 --mem=8000 -J PrepareKallisto -o tmp/PrepareKallisto.out -e tmp/PrepareKallisto.err Scripts/GeneExpression/PrepareFiles.sh

./Scripts/GeneExpression/Geneexpression_fastqc_kallisto.sh

./Scripts/GeneExpression/JoinResultsByGene_Tximport.sh

Orthologs and paralogs analysis

Filtering gene sets

Prepare gene sets for each species.

Scripts:
  • Scripts/FilteringGeneSets/FilteringSetGenesPerSpecies.sh
  • Scripts/FilteringGeneSets/ExtractDNAseqFromGenome.pl # To extract cDNA sequences
Usage:
sbatch -t 10:00:00 --mem=8000 -J FiltGenes -o tmp/FilteringGeneSets.out -e tmp/FilteringGeneSets.err Scripts/FilteringGeneSets/FilteringSetGenesPerSpecies.sh

Find orthologs

Scripts:
  • Scripts/FindOrthologs/FindOrthologs_brocoli.sh
Usage:
sbatch -t 10:00:00 --mem=8000 -J BAmpVertOut -o tmp/Broccoli_AmphVertebOutDeut.out -e tmp/Broccoli_AmphVertebOutDeut.err conda run -n broccoli Scripts/FindOrthologs/FindOrthologs_brocoli.sh AmphVertebOutDeut
sbatch -t 03:00:00 --mem=8000 -J BAmpVert -o tmp/Broccoli_AmphVerteb.out -e tmp/Broccoli_AmphVerteb.err conda run -n broccoli Scripts/FindOrthologs/FindOrthologs_brocoli.sh AmphVerteb