Annotation - Olurida_v081 MAKER ID Mapping

2019
Olympia Oyster Genome Sequencing
Author

Sam White

Published

January 8, 2019

After getting through the initial MAKER annotation and SNAP gene predictions, I needed (wanted?) to simplify annotation names that will be easier to read and are in a more standardized format; similiar to NCBI.

MAKER provides this functionality.

Ran the following SBATCH script on Mox:


#!/bin/bash
## Job Name
#SBATCH --job-name=maker
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=15-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/outputs/20190108_oly_maker_id_mapping

# Load Python Mox module for Python module availability

module load intel-python3_2017

# Load Open MPI module for parallel, multi-node processing

module load icc_19-ompi_3.1.2

# SegFault fix?
export THREADS_DAEMON_MODEL=1

# Document programs in PATH (primarily for program version ID)

date >> system_path.log
echo "" >> system_path.log
echo "System PATH for $SLURM_JOB_ID" >> system_path.log
echo "" >> system_path.log
printf "%0.s-" {1..10} >> system_path.log
echo ${PATH} | tr : \\n >> system_path.log

# Variables
maker_dir=/gscratch/srlab/programs/maker-2.31.10/bin

maker_prot_fasta=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.maker.proteins.fasta
maker_transcripts_fasta=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.maker.transcripts.fasta
snap02_gff=/gscratch/scrubbed/samwhite/outputs/20181127_oly_maker_genome_annotation/snap02/20181127_oly_genome_snap02.all.gff

cp ${maker_prot_fasta} 20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta
cp ${maker_transcripts_fasta} 20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta
cp ${snap02_gff} 20181127_oly_genome_snap02.all.renamed.gff

# Run MAKER programs
## Change gene names
${maker_dir}/maker_map_ids \
--prefix OLUR_ \
--justify 8 \
${snap02_gff} \
> 20181127_oly_genome.map

## Map GFF IDs
${maker_dir}/map_gff_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.renamed.gff

## Map FastAs
### Proteins
${maker_dir}/map_fasta_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta

### Transcripts
${maker_dir}/map_fasta_ids \
20181127_oly_genome.map \
20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta

RESULTS

Output folder:

Mapping file (text):

Renamed GFF:

Renamed protein FastA:

Renamed transcripts FastA:

Here’s a look at the files to show that this worked.

  • Map file
This files is used as a key for the name conversions, original names on left, new names on right

head map file
  • Proteins FastA
Note the name update at the beginning of the FastA descriptions: Olurida_#########-RA

head proteins FastA
  • Transcripts FastA
Note the name update at the beginning of the FastA descriptions: Olurida_#########-RA

head transcripts FastA
  • GFF
The new IDs are present but only shown for gene models:

head GFF

gene models GFF

Regardless, the next steps are to use the newly labeled protein FastA file for BLASTp and protein domain identification. Will move forward with those two steps.