# Fasta indexing:
hisat2-build /work/smaman/oct2021_intronSeeker/rerunFRS/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa

# HiSat2 Alignement:
hisat2 -x /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_genomeRef/frs_n1000_r100_mix_cov100X_am_tr_d1_contigs-modified.fa -p 1 -1 /work/smaman/oct2021_intronSeeker/rerunFRS/sr_n1000_r100_mix_cov100X_am_tr_d1_R1.fastq.gz -2 /work/smaman/oct2021_intronSeeker/rerunFRS/sr_n1000_r100_mix_cov100X_am_tr_d1_R2.fastq.gz -q | samtools view -bS | samtools sort -o /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_n1000_r100_mix_cov100X_am_tr_d1.sort.bam

# BAM indexing:
samtools index /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_n1000_r100_mix_cov100X_am_tr_d1.sort.bam /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_n1000_r100_mix_cov100X_am_tr_d1.sort.bai

# BAM flagstat computation:
samtools flagstat --threads 1 /work/smaman/oct2021_intronSeeker/rerunFRS//hisat2_n1000_r100_mix_cov100X_am_tr_d1.sort.bam