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
WorkflowSalmon gene-level differential screen→K-mer gene-level differential screen→K-mer gene-level differential screen v2→K-mer gene-level differential screen v3
Codex GPT-5.5
Replicate 2
Matches predictionUDT + standard tools
AnswerKLF4
WorkflowSalmon→Prepare GENCODE v50 transcript reference→Prepare GENCODE v50 transcript reference v2→UDT render probe→UDT render probe v2→4 more tools
- Total tokens
- 3.9M
- Output
- 17.2K
Codex GPT-5.5
Replicate 3
Matches predictionUDT + standard tools
AnswerKLF4
WorkflowSalmon→Fastq Stats→Rna Star→RNA DE compare GENCODE v49→RNA DE compare GENCODE v49 v2→12 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
WorkflowFastqc→Salmon→Hisat2→Rna Star→Featurecounts→2 more tools
- Total tokens
- 7.9M
- Output
- 14.5K
Codex GPT-5.6 Sol
Replicate 2
Matches predictionUDT + standard tools
AnswerKLF4
WorkflowFastqc→Salmon→Hisat2→Rna Star→Compare 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
WorkflowFastqc→Hisat2→Featurecounts→Join datasets→Add A Column1→1 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
WorkflowNo Galaxy tool job recorded
- Total tokens
- 15.9M
- Output
- 78.5K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Matches predictionStandard tools only
AnswerKLF4
WorkflowUpload1→Rna Star→Featurecounts→Join datasets→Add A Column1→1 more tools
- Total tokens
- 9.9M
- Output
- 33.4K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Matches predictionStandard tools only
AnswerKLF4
- 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
WorkflowFastqc→Hisat2→Featurecounts→Deseq2→Two-sample RNA-seq descriptive contrast→6 more tools
- Total tokens
- 13.2M
- Output
- 42.4K
Codex GPT-5.6 Luna
Replicate 2
Matches predictionUDT + standard tools
AnswerKLF4
WorkflowFastqc→Hisat2→Featurecounts→Tp Sort Header Tool→Join datasets→9 more tools
- Total tokens
- 21.8M
- Output
- 50.8K
Codex GPT-5.6 Luna
Replicate 3
Matches predictionStandard tools only
AnswerKLF4
WorkflowFastqc→Hisat2→Featurecounts→Sort rows→Edger→6 more tools
- Total tokens
- 11.0M
- Output
- 30.6K