Alignment Data

RNA-seq

millipora genome prep

/home/shared/hisat2-2.2.1/hisat2_extract_exons.py \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
> ../output/04-Apulcra-hisat/m_exon.tab

head ../output/04-Apulcra-hisat/m_exon.tab

/home/shared/hisat2-2.2.1/hisat2_extract_splice_sites.py \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
> ../output/04-Apulcra-hisat/m_splice_sites.tab

“\({programs_array[hisat2_build]}" \ "\){genome_fasta}”
“\({genome_index_name}" \ --exon "\){exons}”
–ss “\({splice_sites}" \ -p "\){threads}”
2> hisat2-build_stats.txt

/home/shared/hisat2-2.2.1/hisat2-build \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna \
GCF_013753865.1_Amil_v2.1 \
--exon ../output/04-Apulcra-hisat/m_exon.tab \
--ss ../output/04-Apulcra-hisat/m_splice_sites.tab \
-p 40 \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
2> ../output/04-Apulcra-hisat/hisat2-build_stats.txt

Alignment

Hisat2 alignments “\({programs_array[hisat2]}" \ -x "\){genome_index_name}”
-1 “\({fastq_list_R1}" \ -2 "\){fastq_list_R2}”
-S “\({sample_name}".sam \ 2> "\){sample_name}”-hisat2_stats.txt

/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCF_013753865.1_Amil_v2.1 \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_mil.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats.txt