I am using RNA-seq data taken from Sea Cucumbers (Apostichopus japonicus) that were treated under 2 different temperatures (26°C & 30°C). The purpose being to conduct DGE analysis to determine the biological responses that heat stress induces on this organism. Data was obtained from the NIH website, done by researchers in Qingdao Agricultural University.
Methods: Heat stress experiment
3 controls kept at 18°C
Six 26°C (Sub lethal temperature)
Three 30°C (Lethal temperature)
Sea cucumbers went through a temperature-rise process from 18°C to 26°C or to 30°C respectively, with a rate of 2°C per hour by using a heating rod.
Maintained at 26°C temperature for 6 hours and 48 hours.
The 30°C treatment groups were only kept at that temperature for 6 hours (likely due to lethality).
Set input and output directoriesINPUT_DIR="/home/shared/8TB_HDD_02/hannia/SeaCucumber/PRJNA848687_fastq"OUTPUT_DIR="/home/shared/8TB_HDD_02/hannia/SeaCucumber/output/kallisto_01"INDEX="/home/shared/8TB_HDD_02/hannia/SeaCucumber/index.idx"KALLISTO="/home/shared/kallisto/kallisto"Loop through all forward reads (_1.fastq)for R1 in${INPUT_DIR}/*_1.fastq;doExtract the base sample ID (e.g., SRR19635628)SAMPLE=$(basename"$R1" _1.fastq)Define the reverse readR2="${INPUT_DIR}/${SAMPLE}_2.fastq"Create output directory for this sampleSAMPLE_OUT="${OUTPUT_DIR}/${SAMPLE}"mkdir-p"$SAMPLE_OUT"Run kallisto quant"$KALLISTO" quant -i"$INDEX"-o"$SAMPLE_OUT"-t 40 "$R1""$R2"
2. Creating abundance estimates for gene expression matrix.
