mkdir hisat2

cp chr8.fna ../hisat2

hisat2-build chr8.fna chr8

mkdir rna-seq

cp ../DATA/rna_reads/SRR2015718_1.fastq.gz

cp ../../DATA/rna_reads/SRR2015718_1.fastq.gz ../../lidia/rna-seq

fastqc SRR2015718_1.fastq.gz

cp SRR2015718_1_fastqc.html ~/public_html/term3/block3/pr14

hisat2 -p 10 -x chr8 -k 3 -U SRR2015718_1.fastq.gz > mapped_reads_rna.sam 2> log_hisat2.txt

samtools sort -o mapped_reads_rna.bam mapped_reads_rna.sam

samtools index mapped_reads_rna.bam

samtools view -h mapped_reads_rna.bam NC_000008.11 > reads_chr8.sam
samtools sort -o reads_chr8.bam reads_chr8.sam

cp ../../DATA/genes/gencode.chr8.gtf ../../lidia/rna-seq

htseq-count -f bam -s no -t exon reads_chr8.bam gencode.chr8.gtf -o htseq-count_chr8.sam 1> htseq_chr8.txt 2> log_htseq.txt

wc -l htseq_chr8.txt | head -n $lines-5 htseq_chr8.txt | awk '{s+=$2}END{print s}'

tail htseq_chr8.txt

cp log_htseq.txt ~/public_html/term3/block3/pr14

cp log_hisat2.txt ~/public_html/term3/block3/pr14