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CompBioBench item

gene-fusion-q1

Question

You are given paired-end RNA sequencing FASTQ files (gene.fusion.q1.R1.fq.gz, gene.fusion.q1.R2.fq.gz) from human. The data contains a synthetic gene fusion event. Your task is to identify the fusion genes. Report the answer as the names of the two genes joined by a hyphen, with the 5′ partner first and the 3′ partner second, written in all uppercase letters, HGNC symbols. For example: TCF21-COL1A1

Predicted answer
GAPDH-SOX2Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Transcriptomics
Question style
Synthetic/Augmented Data

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArriba
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
AnswerGAPDH-SOX2
Workflow
FASTQ Diagnostic Gene Fusion Q1UDT Path Probe Gene Fusion Q1UDT Path Probe Gene Fusion Q1 v2Kallisto QuantPizzly
Total tokens
2.0M
Output
14.7K
Codex GPT-5.5

Replicate 3

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArribaArriba Get Filters
Total tokens
988.0K
Output
9.5K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArribaTp Grep Tool
Total tokens
7.7M
Output
10.9K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArriba
Total tokens
14.8M
Output
12.1K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
FastqcRna StarArribaFilter rows
Total tokens
17.9M
Output
17.6K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna Star
Total tokens
4.3M
Output
27.6K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Converter Gz To UncompressedRna Star
Total tokens
7.8M
Output
34.8K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArriba
Total tokens
3.6M
Output
18.3K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
FastqcRna Star
Total tokens
19.1M
Output
40.4K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Rna StarArriba
Total tokens
6.8M
Output
25.0K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerGAPDH-SOX2
Workflow
Upload1Fastq StatsRna StarArriba
Total tokens
5.1M
Output
22.5K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeBLASTNMinimap2Bowtie2BWA-MEM2 more tools
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2Bowtie2BWA-MEMBLASTN2 more tools
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeBWA-MEMMinimap2Bowtie2BLASTN2 more tools

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMSamtools
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools1 more tools
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools2 more tools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeBWA-MEMMinimap2Bowtie2Samtools3 more tools
Total tokens
2.8M
Output
34.1K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codePythonMinimap2BLASTNSamtools2 more tools
Total tokens
2.3M
Output
18.9K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeBWA-MEMBowtie2Minimap2Samtools3 more tools
Total tokens
640.5K
Output
13.7K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMSamtoolsBLASTN3 more tools
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMBowtie2Samtools3 more tools
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codeMinimap2BWA-MEMSamtoolsBedtools2 more tools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerGAPDH-SOX2
Workflow
Local codePythonMinimap2BWA-MEMBowtie23 more tools
Total tokens
502.8K
Output
3.1K