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