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Step 1. Download the reference geonme hg38 and build index using STAR

Download both the gtf and fasta file of hg38 and run STAR index built mode. The code to run STAR is in "build_index.sh"

The fasta file is "/QRISdata/Q5755/hg38/hg38.fa" and the annotation file is "/QRISdata/Q5755/hg38/gencode.v43.annotation.gtf"

Step 2. Map the single-end clean reads to hg38

The codes for this step is in "run_mapping.sh"

The sample file is "QRISdata/Q5755/SHOR-0013/fastq_files/230201_NS500239_0527_AH7HGVBGXL_0_mask_short_adapter_reads/SAL_1_S7_R1_001.fastq.gz"

Step 3. Summarize the results from STAR

The codes for this step is in "sum.py". The output file from STAR is named "out_prefixReadsPerGene.out.tab"

Step 4. Create the heatmap

The codes for this step is in "heatmap.py". The codes uses the output from step 3 "sum_gene.csv" to creat the heatmap