add read count script

workflow/scripts/countreads.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# Set reference files
+GFF_FILE="resources/reference/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3"
+
+# Sample names
+SAMPLES=("Kisumu1" "Kisumu2" "Kisumu3" "Kisumu4" "G28-BusiaSurvivors1" "G28-BusiaSurvivors2" "G28-BusiaSurvivors3" "G28-BusiaSurvivors4")
+
+# Loop through each sample and run the tools
+for SAMPLE in "${SAMPLES[@]}"
+do
+    BAM_FILE="results/alignments/${SAMPLE}.hisat2.bam"
+    R1_FASTQ="resources/reads/${SAMPLE}_1.fastq"
+    R2_FASTQ="resources/reads/${SAMPLE}_2.fastq"
+
+    FEATURECOUNTS_OUTPUT="${SAMPLE}_featureCounts_output.txt"
+    HTSEQCOUNT_OUTPUT="${SAMPLE}_htseq_counts_output.txt"
+    KALLISTO_OUTPUT="${SAMPLE}_kallisto_output"
+
+    # Run featureCounts
+    echo "Running featureCounts for ${SAMPLE}..."
+    featureCounts -a $GFF_FILE -o $FEATURECOUNTS_OUTPUT -p -B -t exon -g Parent -C $BAM_FILE
+    if [ $? -ne 0 ]; then
+        echo "featureCounts failed for ${SAMPLE}"
+        exit 1
+    fi
+
+    # Run htseq-count
+    echo "Running htseq-count for ${SAMPLE}..."
+    htseq-count -f bam -r pos -s no -t exon -i Parent $BAM_FILE $GFF_FILE > $HTSEQCOUNT_OUTPUT
+    if [ $? -ne 0 ]; then
+        echo "htseq-count failed for ${SAMPLE}"
+        exit 1
+    fi
+
+done
+
+echo "All tools have completed successfully for all samples."