added synthetic fastqs for fusion detection

Author: khersameesh24

fastqs/generate_synthetic_fastqs.sh

@@ -0,0 +1,102 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+FASTA="minigenome.fa"
+OUTDIR="synthetic_reads"
+
+mkdir -p "$OUTDIR"/{genes,fusions}
+
+echo "====================================="
+echo "Step 1: index FASTA"
+echo "====================================="
+samtools faidx "$FASTA"
+
+echo "====================================="
+echo "Step 2: define gene list (NO coordinates)"
+echo "====================================="
+
+GENES=(
+  AKAP9 ALK ATF1 BRAF BRD4 CD74 EML4 ETV1 ETV6
+  EWSR1 FLI1 HOOK3 NTRK3 NUTM1 RET ROS1 TMPRSS2
+)
+
+echo "====================================="
+echo "Step 3: build normal gene transcripts"
+echo "====================================="
+
+for gene in "${GENES[@]}"; do
+  seq=$(samtools faidx "$FASTA" "$gene" | tail -n +2)
+
+  echo ">${gene}_normal" > "$OUTDIR/genes/${gene}.fa"
+  echo "$seq" >> "$OUTDIR/genes/${gene}.fa"
+done
+
+cat "$OUTDIR"/genes/*.fa > "$OUTDIR/all_genes.fa"
+
+echo "====================================="
+echo "Step 4: build fusion transcripts"
+echo "====================================="
+
+FUSIONS=(
+  "ALK EML4"
+  "ROS1 CD74"
+  "RET NTRK3"
+  "BRAF ETV6"
+  "EWSR1 FLI1"
+  "TMPRSS2 ALK"
+)
+
+i=0
+for pair in "${FUSIONS[@]}"; do
+  g1=$(echo $pair | awk '{print $1}')
+  g2=$(echo $pair | awk '{print $2}')
+
+  seq1=$(samtools faidx "$FASTA" "$g1" | tail -n +2)
+  seq2=$(samtools faidx "$FASTA" "$g2" | tail -n +2)
+
+  mid1=$(( ${#seq1} / 2 ))
+  mid2=$(( ${#seq2} / 3 ))
+
+  fusion_seq="${seq1:0:$mid1}${seq2:$mid2}"
+
+  echo ">fusion_${g1}_${g2}_${i}" > "$OUTDIR/fusions/fusion_${i}.fa"
+  echo "$fusion_seq" >> "$OUTDIR/fusions/fusion_${i}.fa"
+
+  i=$((i+1))
+done
+
+cat "$OUTDIR"/fusions/*.fa > "$OUTDIR/all_fusions.fa"
+
+echo "====================================="
+echo "Step 5: combine transcriptome"
+echo "====================================="
+
+cat "$OUTDIR/all_genes.fa" "$OUTDIR/all_fusions.fa" > "$OUTDIR/transcriptome.fa"
+
+echo "====================================="
+echo "Step 6: simulate reads"
+echo "====================================="
+
+art_illumina \
+  -ss HS25 \
+  -i "$OUTDIR/all_genes.fa" \
+  -p -l 150 -f 30 -m 200 -s 10 -rs 42 \
+  -o "$OUTDIR/normal_"
+
+art_illumina \
+  -ss HS25 \
+  -i "$OUTDIR/all_fusions.fa" \
+  -p -l 150 -f 5 -m 200 -s 10 -rs 42 \
+  -o "$OUTDIR/fusion_"
+
+echo "====================================="
+echo "Step 7: merge reads"
+echo "====================================="
+
+cat "$OUTDIR/normal_1.fq" "$OUTDIR/fusion_1.fq" > "$OUTDIR/final_1.fq"
+cat "$OUTDIR/normal_2.fq" "$OUTDIR/fusion_2.fq" > "$OUTDIR/final_2.fq"
+
+gzip -f "$OUTDIR/final_1.fq"
+gzip -f "$OUTDIR/final_2.fq"
+
+echo "DONE"