Update read2CNV.slurm

Codes/read2CNV.slurm

 #!/bin/bash
 #SBATCH --job-name=Mo12_2014
-#SBATCH --output=/shared/home/righettin/Analyses/slurm_outputs/Mo12_2014/Mo12_2014.out
-#SBATCH --error=/shared/home/righettin/Analyses/slurm_outputs/Mo12_2014/Mo12_2014.error
+#SBATCH --output=/Analyses/slurm_outputs/Mo12_2014/Mo12_2014.out
+#SBATCH --error=/Analyses/slurm_outputs/Mo12_2014/Mo12_2014.error
 #SBATCH --cpus-per-task=48
 #SBATCH --nodes=1
 
@@ -9,11 +9,11 @@
 genome="Mo12_2014"   # Declaring the genome ID variable
 fr_ln="150"   # Declaring the fragment length used for sequencing
 autosome_sum_length="2937639396"   # Declaring the sum of the length of all autosomes in the reference, third column of the Data/References/hg38/hg38.ungapped.lengths file
-hg38_genome_txt="/shared/home/righettin/Data/References/hg38/hg38.genome.txt"
-hg38_genes_protein_coding_bed="/shared/home/righettin/Data/References/hg38/hg38_genes_protein_coding_tabdelimited.bed"
+hg38_genome_txt="/Data/References/hg38/hg38.genome.txt"
+hg38_genes_protein_coding_bed="/Data/References/hg38/hg38_genes_protein_coding_tabdelimited.bed"
 
 echo "Performing the pipeline for $genome sequenced with fragment lenght equals to $fr_ln bp and mapped to the reference hg38.
-All necessary packages and programs are installed in the conda environmente named "CNVconda", all scripts are in /shared/home/righettin/Scripts directory."
+All necessary packages and programs are installed in the conda environmente named "CNVconda", all scripts are in /Scripts directory."
 
 
 # SECTION A: READS MAPPING
@@ -30,24 +30,24 @@ The output is then processed through some filters."
 # 1.a) Alignment to the Reference Genome
 echo "1.a) Mapping of $genome on hg38:"
 
-bwa aln -t 48 -l 16500 -n 0.01 -o 2 /shared/home/righettin/Data/References/hg38/bwa_2021/hg38 /shared/home/righettin/Data/FASTQ_Files/$genome/${genome}.fastq > /shared/home/righettin/Analyses/mapping/$genome/${genome}_mapped_hg38_multi.sai
+bwa aln -t 48 -l 16500 -n 0.01 -o 2 /Data/References/hg38/bwa_2021/hg38 /Data/FASTQ_Files/$genome/${genome}.fastq > /Analyses/mapping/$genome/${genome}_mapped_hg38_multi.sai
 
 echo "Mapping completed."
 
 # 1.b) Format Conversion
-echo "1.b) Format convertion:"/shared/home/righettin/Data/References/hg38/hg38.genome.txt
-bwa samse /shared/home/righettin/Data/References/hg38/bwa_2021/hg38 /shared/home/righettin/Analyses/mapping/$genome/${genome}_mapped_hg38_multi.sai /shared/home/righettin/Data/FASTQ_Files/$genome/${genome}.fastq \
+echo "1.b) Format convertion:"/Data/References/hg38/hg38.genome.txt
+bwa samse /Data/References/hg38/bwa_2021/hg38 /Analyses/mapping/$genome/${genome}_mapped_hg38_multi.sai /Data/FASTQ_Files/$genome/${genome}.fastq \
 | samtools view -F 4 -h -Su \
-| samtools sort -o /shared/home/righettin/Analyses/mapping/$genome/${genome}.bam
+| samtools sort -o /Analyses/mapping/$genome/${genome}.bam
 
 echo "Format convertion completed."
 
 # 2) Filter Out PCR Duplicates
 echo "2) Filtering out PCR duplicates:"
 
-java -jar /shared/home/righettin/Programs/picard.jar MarkDuplicates --INPUT /shared/home/righettin/Analyses/mapping/$genome/${genome}.bam \
-	--OUTPUT /shared/home/righettin/Analyses/mapping/$genome/${genome}_nopcr.bam \
-	--METRICS_FILE /shared/home/righettin/Analyses/mapping/$genome/${genome}_pcr_duplicates.metrics \
+java -jar /Programs/picard.jar MarkDuplicates --INPUT /Analyses/mapping/$genome/${genome}.bam \
+	--OUTPUT /Analyses/mapping/$genome/${genome}_nopcr.bam \
+	--METRICS_FILE /Analyses/mapping/$genome/${genome}_pcr_duplicates.metrics \
 	--REMOVE_DUPLICATES true \
 	--REMOVE_SEQUENCING_DUPLICATES true
 
@@ -57,23 +57,23 @@ echo "PCR duplicates removed."
 # 3) Filter Reads with Percentage of Identity < than 90% and Shorter than 30bp
 echo "3.a) Bed File Generation and Mismatch Calculation to remove reads with percentage of identity lower than 90% and shorter than 30bp:"
 
-bedtools bamtobed -ed -i /shared/home/righettin/Analyses/mapping/$genome/${genome}_nopcr.bam > /shared/home/righettin/Analyses/mapping/$genome/${genome}_ed.bed
+bedtools bamtobed -ed -i /Analyses/mapping/$genome/${genome}_nopcr.bam > /Analyses/mapping/$genome/${genome}_ed.bed
 
 echo "Bed File created."
 
 echo "3.b) Calculating Read Lenght and Percentage of Mismatches:"
 
-awk -F"\t" '{print $1"\t"$3-$2"\t"$5"\t"($5/($3-$2)*100)"\t"$4}' /shared/home/righettin/Analyses/mapping/$genome/${genome}_ed.bed > /shared/home/righettin/Analyses/mapping/$genome/${genome}_read_length_mismatches.txt
+awk -F"\t" '{print $1"\t"$3-$2"\t"$5"\t"($5/($3-$2)*100)"\t"$4}' /Analyses/mapping/$genome/${genome}_ed.bed > /Analyses/mapping/$genome/${genome}_read_length_mismatches.txt
 
 echo "Read Lenght and Percentage of Mismatches calculated."
 
 echo "3.c) Filtering Out Reads with Percentage of Identity Lower than 90% and shorter than 30bp:"
 
-awk '($4 <= 10) && ($2 >=30) {print $5}' /shared/home/righettin/Analyses/mapping/$genome/${genome}_read_length_mismatches.txt > /shared/home/righettin/Analyses/mapping/$genome/${genome}_filtered_read_names_30bp.txt
-java -jar /shared/home/righettin/Programs/picard.jar FilterSamReads \
-	--INPUT /shared/home/righettin/Analyses/mapping/$genome/${genome}_nopcr.bam \
-	--OUTPUT /shared/home/righettin/Analyses/mapping/$genome/${genome}_nopcr_90perc_30bp.bam \
-	--READ_LIST_FILE /shared/home/righettin/Analyses/mapping/$genome/${genome}_filtered_read_names_30bp.txt \
+awk '($4 <= 10) && ($2 >=30) {print $5}' /Analyses/mapping/$genome/${genome}_read_length_mismatches.txt > /Analyses/mapping/$genome/${genome}_filtered_read_names_30bp.txt
+java -jar /Programs/picard.jar FilterSamReads \
+	--INPUT /Analyses/mapping/$genome/${genome}_nopcr.bam \
+	--OUTPUT /Analyses/mapping/$genome/${genome}_nopcr_90perc_30bp.bam \
+	--READ_LIST_FILE /Analyses/mapping/$genome/${genome}_filtered_read_names_30bp.txt \
 	--FILTER includeReadList
 echo "Reads with Percentage of Identity Lower than 90% and shorter than 30bp removed."
 
@@ -102,15 +102,15 @@ In this second section the de-novo mapping is used to perform the following step
 # 0) Create all necessary directories and subdirectories
 echo "0) Creating all necessary directories and subdirectories:"
 
-mkdir -p /shared/home/righettin/Analyses/Data_preparation/$genome/{avgdepth,bam,corrected,coverage}
+mkdir -p /Analyses/Data_preparation/$genome/{avgdepth,bam,corrected,coverage}
 
 echo "Directories and subdirectories created."
 
 # 1) BAM handling
 echo "1) Separating the BAM obtained with Section A in single chromosome files:"
 
-input_dir="/shared/home/righettin/Analyses/mapping/$genome"
-output_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/bam"
+input_dir="/Analyses/mapping/$genome"
+output_dir="/Analyses/Data_preparation/$genome/bam"
 INPUT_BAM="${input_dir}/${genome}_nopcr_90perc_30bp.bam"
 
 # Index the input BAM file if not already indexed
@@ -133,12 +133,12 @@ echo "BAM separated in single chromosome files. Results are store in $output_dir
 # 2) Correct GC bias
 echo "2) Correcting the BAM files based on GC-bias:"
 
-data_dir="/shared/home/righettin/Analyses/Data_preparation/$genome"
+data_dir="/Analyses/Data_preparation/$genome"
 bam_dir="$data_dir/bam"   # Path to the single chromosomes BAM files created in step 1 
 corrected_dir="$data_dir/corrected"   # Where the corrected BAMs will be stored
-chrom_size_file="/shared/home/righettin/Data/References/hg38/hg38.genome.txt"   # Chromosome size file
-chrom_2bit_dir="/shared/home/righettin/Data/References/hg38/dna_sm"   # 2bit reference genome directory
-blacklist_file="/shared/home/righettin/Data/References/hg38/intervals/blacklist.bed"   # Path to blacklist.bed file
+chrom_size_file="/Data/References/hg38/hg38.genome.txt"   # Chromosome size file
+chrom_2bit_dir="/Data/References/hg38/dna_sm"   # 2bit reference genome directory
+blacklist_file="/Data/References/hg38/intervals/blacklist.bed"   # Path to blacklist.bed file
 
 for bam_file in "$bam_dir"/*.bam; do
     filename=$(basename "$bam_file")   # Extract BAM filename
@@ -171,7 +171,7 @@ echo "The output txt files of the correctGCBias are store in $corrected_dir/freq
 # 3) Compute Depth of Coverage
 echo "3) Computing Depth of Coverage for each Chromosome:"
 
-data_dir="/shared/home/righettin/Analyses/Data_preparation/$genome"
+data_dir="/Analyses/Data_preparation/$genome"
 corrected_dir="$data_dir/corrected"
 coverage_dir="$data_dir/coverage"
 
@@ -193,9 +193,9 @@ echo "Depth of coverage for each chromosome computed. Results are stored in $cov
 # 4) Compute the Average Depth of Coverage for each Chromosome
 echo "4a) Computing Depth of Coverage for each Chromosome:"
 
-coverage_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/coverage"
-avgdepth_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/avgdepth"
-chrom_size_file="/shared/home/righettin/Data/References/hg38/hg38.genome.txt"
+coverage_dir="/Analyses/Data_preparation/$genome/coverage"
+avgdepth_dir="/Analyses/Data_preparation/$genome/avgdepth"
+chrom_size_file="/Data/References/hg38/hg38.genome.txt"
 
 for coverage_file in "$coverage_dir"/*.per-base.bed.gz; do
     filename=$(basename "$coverage_file")   # Extract coverage filename
@@ -217,11 +217,11 @@ echo "Average Depth of Coverage estimated. Results are stored in $avgdepth_dir."
 # 5) Compute the Average Depth of Coverage for each Chromosome excluding blacklisted regions (change the chrom_size_file)
 echo "5) Computing Depth of Coverage for each Chromosome excluding blacklisted regions:"
 
-coverage_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/coverage"
-avgdepth_nobl_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/avgdepth/nobl"
+coverage_dir="/Analyses/Data_preparation/$genome/coverage"
+avgdepth_nobl_dir="/Analyses/Data_preparation/$genome/avgdepth/nobl"
 mkdir -p "$avgdepth_nobl_dir"   # Create avgdepth/nobl directory if it doesn't exist
 blacklist_file="/path/to/blacklist.bed"   # Define blacklist file path
-chrom_size_file="/shared/home/righettin/Data/References/hg38/hg38.ungapped.nobl.lengths"
+chrom_size_file="/Data/References/hg38/hg38.ungapped.nobl.lengths"
 
 for coverage_file in "$coverage_dir"/*.per-base.bed.gz; do
     filename=$(basename "$coverage_file")   # Extract coverage filename
@@ -243,8 +243,8 @@ echo "Average Depth of Coverage estimated. Results are stored in $avgdepth_nobl_
 # 6) Computing Average Depth of Coverage for Autosomes
 echo "6) Computing Average Depth of Coverage for Autosomes:"
 
-coverage_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/coverage"
-genome_doc_file="/shared/home/righettin/Analyses/Data_preparation/$genome/$genome.doc.txt"
+coverage_dir="/Analyses/Data_preparation/$genome/coverage"
+genome_doc_file="/Analyses/Data_preparation/$genome/$genome.doc.txt"
 
 # Loop through autosomes (chromosomes 1 to 22)
 for i in {1..22}; do
@@ -258,17 +258,17 @@ echo "Average Depth of Coverage for Autosomes computed and stored in $genome_doc
 # 7) Computing Coverage of Protein-Coding Genes
 echo "7) Computing Coverage of Protein-Coding Genes:"
 
-coverage_dir="/shared/home/righettin/Analyses/Data_preparation/$genome/coverage"
-genome_dir="/shared/home/righettin/Analyses/Data_preparation/$genome"
+coverage_dir="/Analyses/Data_preparation/$genome/coverage"
+genome_dir="/Analyses/Data_preparation/$genome"
 
 beds=""
 for i in {1..22}; do beds="${beds} $coverage_dir/$genome.hg38.chr${i}.per-base.bed.gz"; done
- bedtools intersect -g /shared/home/righettin/Data/References/hg38/hg38.genome.wout.txt \
- -a /shared/home/righettin/Data/References/hg38/hg38_genes_protein_coding_chr_2_nomt.bed -b ${beds}  \
+ bedtools intersect -g /Data/References/hg38/hg38.genome.wout.txt \
+ -a /Data/References/hg38/hg38_genes_protein_coding_chr_2_nomt.bed -b ${beds}  \
 -wa -wb | gzip -c > $genome_dir/$genome.hg38.genes.protein_coding.coverage.gz
 
-starting_gz=/shared/home/righettin/Analyses/Data_preparation/$genome/$genome.hg38.genes.protein_coding.coverage.gz
-ending_gz=/shared/home/righettin/Analyses/Data_preparation/$genome/$genome.fixed.hg38.genes.protein_coding.coverage.gz
+starting_gz=/Analyses/Data_preparation/$genome/$genome.hg38.genes.protein_coding.coverage.gz
+ending_gz=/Analyses/Data_preparation/$genome/$genome.fixed.hg38.genes.protein_coding.coverage.gz
 
 zcat $starting_gz | sed 's/chr//g' | gzip -c > $ending_gz   # take out "chr" from the file 
 
@@ -276,7 +276,7 @@ zcat $starting_gz | sed 's/chr//g' | gzip -c > $ending_gz   # take out "chr" fro
 echo "Coverage of Protein-Coding Genes computed and stored in /shared/home/righetti/Analyses/Data_preparation/$genome/$genome.hg38.genes.protein_coding.coverage.gz."
 
 # SECTION C: CNVs ESTIMATE
-CNV_estimates_dir="/shared/home/righettin/Analyses/CNV_estimates"
+CNV_estimates_dir="/Analyses/CNV_estimates"
 echo "
 -. .-.   .-. .-.   .-. .-.   .
 ||\|||\ /|||\|||\ /|||\|||\ /|
@@ -290,9 +290,9 @@ In this section CNVs are estimated for each genome. Results are stored in $CNV_e
 # 1) Gene copy number estimates
 echo "Estimating gene CNV for $genome:"
 
-chrom_doc="/shared/home/righettin/Analyses/Data_preparation/$genome/avgdepth/nobl/$genome.hg38.nobl.avgdepth.txt"
-gene_doc="/shared/home/righettin/Analyses/Data_preparation/$genome/$genome.fixed.hg38.genes.protein_coding.coverage.gz"
+chrom_doc="/Analyses/Data_preparation/$genome/avgdepth/nobl/$genome.hg38.nobl.avgdepth.txt"
+gene_doc="/Analyses/Data_preparation/$genome/$genome.fixed.hg38.genes.protein_coding.coverage.gz"
 
-python3 /shared/home/righettin/Scripts/CNV_scripts/computeGeneCopy.py --chrom-doc $chrom_doc --gene-doc $gene_doc > $CNV_estimates_dir/$genome.nobl.cnv.tsv
+python3 /Scripts/CNV_scripts/computeGeneCopy.py --chrom-doc $chrom_doc --gene-doc $gene_doc > $CNV_estimates_dir/$genome.nobl.cnv.tsv
 
 echo "CNV estimated for $genome."