---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Transcriptome Comparison - C.bairdi Transcriptomes Compared with DETONATE on Mox
date: '2020-05-29 09:40'
tags:
  - Tanner crab
  - Chionoecetes bairdi
  - mox
  - DETONATE
  - Carcinus maenas
  - green crab
  - Portunus trituberculatus
  - Japanese blue crab
categories:
  - 2020
  - Miscellaneous
---
We've produced a number of [_C.bairdi_ transcriptomes](https://github.com/RobertsLab/resources/wiki/Genomic-Resources#transcriptomes) and we're interested in doing some comparisons to try to determine which one might be "best". I previously [compared the BUSCO scores of each of these transcriptomes](https://robertslab.github.io/sams-notebook/posts/2020/2020-05-28-Transcriptome-Comparisons-C.bairdi-BUSCO-Scores.html) and now will be using the [DETONATE](http://deweylab.biostat.wisc.edu/detonate) software package to perform two different types of comparisons: compared to a reference ([REF-EVAL](http://deweylab.biostat.wisc.edu/detonate/ref-eval.html)) and determine an overall quality "score" ([RSEM-EVAL](http://deweylab.biostat.wisc.edu/detonate/rsem-eval/)). I'll be running [REF-EVAL](http://deweylab.biostat.wisc.edu/detonate/ref-eval/) in this notebook.

A link to the paper is here and explains both:

- [Evaluation of de novo transcriptome assemblies from RNA-Seq data](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5)

I opted to just "quickly" run through [REF-EVAL](http://deweylab.biostat.wisc.edu/detonate/ref-eval.html), as it only requires (minimally) transcriptome FastAs for performing assembly comparisons; although it probably provides more accurate comparisons if you generate a "true assembly" first. However, this can't always be done if using a publicly available transcriptome which doesn't have the corresponding FastQ files used for the assembly.

Since this is designed to compare a transcriptome assembly to a "reference" transcriptome of a related species, I did a couple of things:

1. Downloaded Japanese blue crab (_Portunus trituberculatus_) transcriptome from NCBI (accession: GFFJ01.1).

2. Downloaded green crab (_Carcinus maenas_) transcriptome from NCBI (accession: GBXE01.1).

3. Downloaded and [assembled _Portunus trituberculatus_ NCBI SRA RNAseq data](https://robertslab.github.io/sams-notebook/posts/2020/2020-05-23-Transcriptome-Assembly---P.trituberculatus-Japanese-blue-crab-NCBI-SRA-BioProject-PRJNA597187-Data-with-Trinity-on-Mox/).

I then compared all of our assemblies to each other, to the three "reference" sequences, and the three "reference" sequences to our _C.bairdi_ assemblies (i.e. using our assemblies as the "reference" in the comparison).

This job was run on Mox.


SBATCH script (GitHub):

- [20200529_cbai_detonate_transcriptome_comparisons.sh](https://github.com/RobertsLab/sams-notebook/blob/f41eb77f8e22c263cf364d536f8b720f6737b8d4/sbatch_scripts/20200529_cbai_detonate_transcriptome_comparisons.sh)

```shell
#!/bin/bash
## Job Name
#SBATCH --job-name=cbai_detonate_transcriptome_comparisons
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=8-00:00:00
## Memory per node
#SBATCH --mem=500G
##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/20200529_cbai_detonate_transcriptome_comparisons


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

# Array of the various comparisons to evaluate
# Each condition in each comparison should be separated by a "-"
transcriptomes_array=(
cbai_transcriptome_v1.0.fa \
cbai_transcriptome_v1.5.fa \
cbai_transcriptome_v1.6.fa \
cbai_transcriptome_v1.7.fa \
cbai_transcriptome_v2.0.fa \
cbai_transcriptome_v3.0.fa \
20200526.P_trituberculatus.Trinity.fa \
GFFJ01.1.fa \
GBXE01.1.fa
)


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

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability

module load intel-python3_2017

# 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


threads=28

#programs
pblat="/gscratch/srlab/programs/pblat-2.1/pblat"
detonate="/gscratch/srlab/programs/detonate-1.11/ref-eval/ref-eval"


# Determine length of transcriptomes array
transcriptomes_array_length=${#transcriptomes_array[@]}

# Loop through each comparison
for (( i=0; i < transcriptomes_array_length; i++ ))
do
  transcriptome1="${transcriptomes_array[$i]}"

  # Capture FastA checksums for verification
  echo "Generating checksum for ${transcriptome1}"
  md5sum "${transcriptome1}" >> fasta.checksums.md5
  echo "Finished generating checksum for ${transcriptome1}"
  echo ""

  for (( j=0; j < transcriptomes_array_length; j++ ))
  do
    # Don't run comparison of the same transcriptome
    if [[ "${transcriptomes_array[$j]}" != "${transcriptomes_array[$i]}" ]]; then
      transcriptome2="${transcriptomes_array[$j]}"
      comparison1="${transcriptome1}-vs-${transcriptome2}"
      comparison2="${transcriptome2}-vs-${transcriptome1}"

      # Check if pblat output files are not present
      if [[ ! -f "${comparison1}.psl" ]] && [[  -f "${comparison2}".psl ]]; then
        # Run pblat
        echo "Starting pblat: ${comparison1}"
        ${pblat} -minIdentity=80 -threads=${threads} "${transcriptome2}" "${transcriptome1}" "${comparison1}".psl
        echo "Finished pblat: ${comparison1}"
        echo ""

        echo "Starting pblat: ${comparison2}"
        ${pblat} -minIdentity=80 -threads=${threads} "${transcriptome1}" "${transcriptome2}" "${comparison2}".psl
        echo "Finished pblat: ${comparison2}"
        echo ""
      fi

      # Check if DETONATE output file exists
      if [[ ! -f "${comparison1}.scores.txt" ]]; then
        # Run ref-eval, unweighted scores only
        echo "Running DETONATE with ${transcriptome1} and ${transcriptome2}."
        ${detonate} \
        --scores=nucl,pair,contig \
        --weighted=no \
        --A-seqs "${transcriptome1}" \
        --B-seqs "${transcriptome2}" \
        --A-to-B "${comparison1}".psl \
        --B-to-A "${comparison2}".psl \
        | tee "${comparison1}.scores.txt"
        echo "Finished DETONATE with ${transcriptome1} and ${transcriptome2}."
        echo ""
      fi
    fi


  done
done
```

---

# RESULTS

Took a bit over 3 days to complete:

![cbai transcriptome comparisons runtime](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20200529_cbai_detonate_transcriptome_comparisons_runtime.png?raw=true)

NOTE: There are two jobs associated with this because I had to modify SBATCH script after initial run to account for missed reference comparisons.

Well, I ran this and I am completely unsure what it all means. Hah! And, ugh! It was easy enough to setup and run, so it didn't require too much effort. However, even after reading [the paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5), it's still not clear if this has any real value; particularly since the paper focuses on evaluating _de novo_ assemblies. The evaluation to a reference transcriptome seems like it's an aside. However, the two sets of software are packaged together as DETONATE, so I figured I'd run them both.

All the files are linked below for anyone curious enough to spend time trying to figure out if these results mean anything...

Output folder:

- [20200529_cbai_detonate_transcriptome_comparisons/](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/)




#### Reference: cbai_transcriptome_v1.0

- [GBXE01.1.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.0.fa.scores.txt)

---

#### Reference: cbai_transcriptome_v1.5

- [GBXE01.1.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.5.fa.scores.txt)

---

#### Reference: cbai_transcriptome_v1.6

- [GBXE01.1.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.6.fa.scores.txt)

---

#### Reference: cbai_transcriptome_v1.7

- [GBXE01.1.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v1.7.fa.scores.txt)

---

#### Reference: cbai_transcriptome_v2.0

- [GBXE01.1.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-cbai_transcriptome_v2.0.fa.scores.txt)

---

#### Reference: cbai_transcriptome_v3.0

- [GBXE01.1.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [GFFJ01.1.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-cbai_transcriptome_v3.0.fa.scores.txt)

---

#### Reference: 20200526.P_trituberculatus

- [GBXE01.1.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [GFFJ01.1.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-20200526.P_trituberculatus.Trinity.fa.scores.txt)

---

#### Reference: GBXE01.1

- [GFFJ01.1.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GFFJ01.1.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-GBXE01.1.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-GBXE01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-GBXE01.1.fa.scores.txt)

---

#### Reference: GFFJ01.1

- [GBXE01.1.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/GBXE01.1.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v1.0.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.0.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v1.5.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.5.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v1.6.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.6.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v1.7.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v1.7.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v2.0.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v2.0.fa-vs-GFFJ01.1.fa.scores.txt)

- [cbai_transcriptome_v3.0.fa-vs-GFFJ01.1.fa.scores.txt](https://gannet.fish.washington.edu/Atumefaciens/20200529_cbai_detonate_transcriptome_comparisons/cbai_transcriptome_v3.0.fa-vs-GFFJ01.1.fa.scores.txt)
