{r setup, include=FALSE} library(knitr) library(tidyverse) knitr::opts_chunk$set( echo = TRUE, # Display code chunks eval = FALSE, # Evaluate code chunks warning = FALSE, # Hide warnings message = FALSE, # Hide messages fig.width = 6, # Set plot width in inches fig.height = 4, # Set plot height in inches fig.align = “center” # Align plots to the center )
RNA-seq
millipora genome prep
{r, engine=‘bash’}
/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
{r, engine=‘bash’} head ../output/04-Apulcra-hisat/m_exon.tab
{r, engine=‘bash’}
/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
{r, engine=‘bash’} /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
{r, engine=‘bash’} /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