Assembly Indexing - C.bairdi Transcriptome cbai_transcriptome_v3.1.fasta with Hisat2 on Mox

2021
Tanner Crab RNAseq
Author

Sam White

Published

September 8, 2021

We recently received reviews back for the Tanner crab paper submission (“Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi)”) and one of the reviewers requested a more in-depth analysis. As part of addressing this, we’ve decided to identify SNPs withing the _Chionoecetes bairdi (Tanner crab) transcriptome used in the paper (cbai_transcriptome_v3.1). Since the process involves aligning sequencing reads to the transcriptome, the first thing that needed to be done was to generate index files for the aligner (HISAT2, in this particular case), so I ran HISAT2 on Mox.

SBATCH script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=20210908-cbai-transcriptome_v3.1-hisat2-build-index
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=5-00:00:00
## Memory per node
#SBATCH --mem=200G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20210908-cbai-transcriptome_v3.1-hisat2-build-index

## Script using HiSat2 to build a transcriptome index for cbai_transcriptome_v3.1 using Hisat2.


###################################################################################
# These variables need to be set by user

## Assign Variables

# Set number of CPUs to use
threads=40

# Set Hisat2 index name
transcriptome_index_name="cbai-transcriptome_v3.1"

# Paths to programs
hisat2_dir="/gscratch/srlab/programs/hisat2-2.1.0"
hisat2_build="${hisat2_dir}/hisat2-build"

# Input/output files
transcriptome_dir="/gscratch/srlab/sam/data/C_bairdi/transcriptomes"
transcriptome_fasta="${transcriptome_dir}/cbai_transcriptome_v3.1.fasta"


# Programs associative array
declare -A programs_array
programs_array=(
[hisat2_build]="${hisat2_build}"
)


###################################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability

module load intel-python3_2017

# Build Hisat2 reference index
"${programs_array[hisat2_build]}" \
"${transcriptome_fasta}" \
"${transcriptome_index_name}" \
-p "${threads}" \
2> hisat2_build.err

# Generate checksums for all files
md5sum * >> checksums.md5

# Copy Hisat2 index files to my data directory for later use
rsync -av "${transcriptome_index_name}"*.ht2 "${transcriptome_dir}"


#######################################################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help
    fi
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
fi


# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

RESULTS

Very quick, just under 4mins:

Mox runtime for Hisat2 index building of cbai-transcriptome_v3.1

Output folder:

Next up, perform the perform the alignments using HISAT2.