readMapping.sh

# This script checks the qualitiy of our fastq files and performs an alignment to the human cDNA transcriptome reference with Kallisto.
# To run this 'shell script' you will need to open your terminal and navigate to the directory where this script resides on your computer.
# This should be the same directory where you fastq files and reference fasta file are found.
# Change permissions on your computer so that you can run a shell script by typing: 'chmod 777 readMapping.sh' (without the quotes) at the terminal prompt 
# Then type './readMapping.sh' (without the quotes) at the prompt.  
# This will begin the process of running each line of code in the shell script.

# first use fastqc to check the quality of our fastq files:
fastqc *.gz -t 4

# next, we want to build an index from our reference fasta file 
# I get my reference mammalian transcriptome files from here: https://useast.ensembl.org/info/data/ftp/index.html
kallisto index -i Homo_sapiens.GRCh38.cdna.all.index Homo_sapiens.GRCh38.cdna.all.fa.gz

# now map reads to the indexed reference host transcriptome
# use as many 'threads' as your machine will allow in order to speed up the read mapping process.
# note that we're also including the '&>' at the end of each line
# this takes the information that would've been printed to our terminal, and outputs this in a log file that is saved in /data/course_data

# first the healthy subjects (HS)
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o HS01 -t 4 --single -l 250 -s 30 SRR8668755.fastq.gz &> HS01.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o HS02 -t 4 --single -l 250 -s 30 SRR8668756.fastq.gz &> HS02.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o HS03 -t 4 --single -l 250 -s 30 SRR8668757.fastq.gz &> HS03.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o HS04 -t 4 --single -l 250 -s 30 SRR8668758.fastq.gz &> HS04.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o HS05 -t 4 --single -l 250 -s 30 SRR8668759.fastq.gz &> HS05.log

# then the cutaneous leishmaniasis (CL) patients
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o CL08 -t 4 --single -l 250 -s 30 SRR8668769.fastq.gz &> CL08.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o CL10 -t 4 --single -l 250 -s 30 SRR8668771.fastq.gz &> CL10.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o CL11 -t 4 --single -l 250 -s 30 SRR8668772.fastq.gz &> CL11.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o CL12 -t 4 --single -l 250 -s 30 SRR8668773.fastq.gz &> CL12.log
kallisto quant -i Homo_sapiens.GRCh38.cdna.all.index -o CL13 -t 4 --single -l 250 -s 30 SRR8668774.fastq.gz &> CL13.log

# summarize fastqc and kallisto mapping results in a single summary html using MultiQC
multiqc -d . 

echo "Finished"