Back to results

CompBioBench item

deg-simple-q1

Question

I have bulk RNA-seq fastq files from 2 human samples (deg.simple.q1.sampleA.fq.gz, deg.simple.q1.sampleB.fq.gz). There is exactly one gene that is strongly differentially expressed between the two samples. Report the HGNC gene symbol (uppercase) for that gene.

Predicted answer
KLF4Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Transcriptomics
Question style
Routine Analysis

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 predictionUDT-only
AnswerKLF4
Workflow
Salmon gene-level differential screenK-mer gene-level differential screenK-mer gene-level differential screen v2K-mer gene-level differential screen v3
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
SalmonPrepare GENCODE v50 transcript referencePrepare GENCODE v50 transcript reference v2UDT render probeUDT render probe v24 more tools
Total tokens
3.9M
Output
17.2K
Codex GPT-5.5

Replicate 3

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
SalmonFastq StatsRna StarRNA DE compare GENCODE v49RNA DE compare GENCODE v49 v212 more tools
Total tokens
11.0M
Output
23.7K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
FastqcSalmonHisat2Rna StarFeaturecounts2 more tools
Total tokens
7.9M
Output
14.5K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
FastqcSalmonHisat2Rna StarCompare STAR gene counts with GENCODE symbols
Total tokens
48.1M
Output
27.7K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionStandard tools only
AnswerKLF4
Workflow
FastqcHisat2FeaturecountsJoin datasetsAdd A Column11 more tools
Total tokens
10.9M
Output
17.0K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
No Galaxy tool job recorded
Total tokens
15.9M
Output
78.5K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerKLF4
Workflow
Upload1Rna StarFeaturecountsJoin datasetsAdd A Column11 more tools
Total tokens
9.9M
Output
33.4K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerKLF4
Workflow
Salmon
Total tokens
17.5M
Output
45.8K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
FastqcHisat2FeaturecountsDeseq2Two-sample RNA-seq descriptive contrast6 more tools
Total tokens
13.2M
Output
42.4K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionUDT + standard tools
AnswerKLF4
Workflow
FastqcHisat2FeaturecountsTp Sort Header ToolJoin datasets9 more tools
Total tokens
21.8M
Output
50.8K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerKLF4
Workflow
FastqcHisat2FeaturecountsSort rowsEdger6 more tools
Total tokens
11.0M
Output
30.6K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2Python
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2SamtoolsPython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2SamtoolsPython
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerKLF4
Workflow
Local codeMinimap2Samtools
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2Samtools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerKLF4
Workflow
Local codePythonSamtoolsBowtie2BWA-MEM3 more tools
Total tokens
1.4M
Output
9.6K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerKLF4
Workflow
Local codeMinimap2SamtoolsPythonpysam1 more tools
Total tokens
375.4K
Output
11.9K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerKLF4
Workflow
Local codePythonBowtie2SamtoolsSciPy5 more tools
Total tokens
2.0M
Output
20.9K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2SamtoolsPython2 more tools
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerKLF4
Workflow
Local codeBowtie2Minimap2SamtoolsPython3 more tools
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerKLF4
Workflow
Local codeBWA-MEMBowtie2Minimap2Samtools2 more tools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerKLF4
Workflow
Local codePythonMinimap2Bowtie2Samtools2 more tools
Total tokens
512.5K
Output
3.7K