A pulcra HiSat2

#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

#!/bin/bash

# This script will extract splice sites from the gtf file

# This is the command to extract splice sites from the gtf file
/home/shared/hisat2-2.2.1/hisat2_extract_splice_sites.py \

# This is the gtf file
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \

# This is the output file
> ../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

#!/bin/bash

# hisat2-build is a program that builds a hisat2 index for the reference genome
# ../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna is the reference genome
# GCF_013753865.1_Amil_v2.1 is the name of the index
# --exon ../output/04-Apulcra-hisat/m_exon.tab is the exon file
# --ss ../output/04-Apulcra-hisat/m_splice_sites.tab is the splice site file
# -p 40 is the number of threads
# ../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf is the gtf file
# 2> ../output/04-Apulcra-hisat/hisat2-build_stats.txt is the output file

/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

1 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

#!/bin/bash comment with GPT Studio

# run hisat2 to align reads to the reference genome
/home/shared/hisat2-2.2.1/hisat2 \

# specify the reference genome
-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

1.0.1 chatgpt comment test - same chunk as above

this with ChatGPT not inline

This R code is actually a command-line script written in Bash which can be run in the terminal or within an R script using the system() or system2() commands. It runs the program HISAT2 with specific options and parameters on paired-end RNA-seq data for a specific species of organism called Acanthopleura granulata (also known as Acmaea intestinalis) to align the sequencing reads to its reference genome.

---

ChatGPT output:

This code is running the HISAT2 alignment tool, which is used to align RNA sequencing reads to a reference genome. It is specifying the following options:

-x specifies the reference genome index to use for the alignment.

-p specifies the number of CPU cores to use in the alignment.

-1 and -2 specify the input paired-end fastq read files to align.

-S specifies the output SAM file to save the alignment results.

2>&1 | tee specifies that both stdout and stderr are to be written to a file ../output/04-Apulcra-hisat/hisat2_stats.txt, while also being printed to the console for the user to see.

The code is assuming that the input fastq files are located at ../data/SRR8601366_1.fastq and ../data/SRR8601366_2.fastq, and that the reference genome index is located at /home/shared/hisat2-2.2.1/hisat2.

The aligned output will be saved to a SAM file located at ../output/04-Apulcra-hisat/SRR8601366_mil.sam.

/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

/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

/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

2 Align with no splice sites

/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_nosplice \
-p 48 \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2-build_stats_nosplice.txt

/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCF_013753865.1_Amil_v2.1_nosplice \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_mil_nosplice.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats_nosplice.txt

3 A hyacinthus

3.1 no splice

/home/shared/hisat2-2.2.1/hisat2-build \
../data/Ahya/ncbi_dataset/data/GCA_020536085.1/GCA_020536085.1_Ahyacinthus.chrsV1_genomic.fna \
../output/04-Apulcra-hisat/GCA_020536085.1_Ahya_nosplice \
-p 48 \
2> ../output/04-Apulcra-hisat/hisat2-build_stats_Ahya_nosplice.txt

/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCA_020536085.1_Ahya_nosplice \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_hya_nosplice.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats_Ahya_nosplice.txt

4 A digitera

/home/shared/hisat2-2.2.1/hisat2_extract_exons.py \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/genomic.gtf \
> ../output/04-Apulcra-hisat/d_exon.tab

/home/shared/hisat2-2.2.1/hisat2_extract_splice_sites.py \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/genomic.gtf \
> ../output/04-Apulcra-hisat/d_splice_sites.tab

/home/shared/hisat2-2.2.1/hisat2-build \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/GCF_000222465.1_Adig_1.1_genomic.fna \
../output/04-Apulcra-hisat/GCF_000222465.1_Adig \
--exon ../output/04-Apulcra-hisat/d_exon.tab \
--ss ../output/04-Apulcra-hisat/d_splice_sites.tab \
-p 48 \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/genomic.gtf \
2> ../output/04-Apulcra-hisat/hisat2-build_stats_Adig.txt

/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCF_000222465.1_Adig \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_dig.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats_dig.txt

4.1 dig no splice

/home/shared/hisat2-2.2.1/hisat2-build \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/GCF_000222465.1_Adig_1.1_genomic.fna \
../output/04-Apulcra-hisat/GCF_000222465.1_Adig_nosplice \
-p 48 \
2> ../output/04-Apulcra-hisat/hisat2-build_stats_Adig.txt

/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCF_000222465.1_Adig_nosplice \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_dig_nosplice.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats_dig_nosplice.txt