Bat gene expression matrix

This instruction only for the Egyptian fruit bat (Rousettus aegyptiacus)

1. Build hisat2 index: 1-work-build_all_index.sh
2. QC, mapping and then calculate FPKM: 2-work-mapping_each_sample.sh
3. Count the FPKM of all samples: 3-work-make_summary.sh
4. Usage
   1. Generate 2-work-mapping_each_sample.sh with the sample_name, reads1 path, reads2 path (FASTQ) of all samples and use the parameters given by ignition.sh (8 cores, 2G ARM), the script automatically clears all the intermediate large files generated in temp.
   2. Run 3-work-make_summary.sh locally to count all the results, and save as a CSV file: output/merged_htc.csv.
5. Running Time: Each sample takes less than 20 minutes.