Question
I have bulk RNA-seq fastq files from 2 human samples (deg.simple.q2.sampleA.fq.gz, deg.simple.q2.sampleB.fq.gz). There is exactly one gene that has differentially expressed isoforms in the 2 samples. Report the HGNC gene symbol (uppercase) for that gene.
- Inferred answer
DEFB110Uniquely inferred 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
CorrectUDT + standard tools
AnswerDEFB110
WorkflowSalmon→Isoform switch Salmon analysis→Salmon runtime probe→Salmon runtime probe compiler→Python Salmon runtime probe→6 more tools
Codex GPT-5.5
Replicate 2
CorrectUDT-only
AnswerDEFB110
WorkflowFASTQ diagnostic sample→Runtime tool probe→Isoform usage by GENCODE transcript alignment
- Total tokens
- 621.2K
- Output
- 9.6K
Codex GPT-5.5
Replicate 3
CorrectUDT + standard tools
AnswerDEFB110
WorkflowFASTQ inspect q2→FASTQ inspect q2 v2→Salmon→Fastq Stats→Grep
- Total tokens
- 7.7M
- Output
- 27.1K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectUDT + standard tools
AnswerDEFB110
WorkflowFastqc→Salmon→Rank differential isoform usage→Rna Star→Rank splice junction usage changes
- Total tokens
- 18.9M
- Output
- 25.4K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
AnswerDEFB110
WorkflowFastqc→Salmon→Kallisto Quant→Compare isoform usage GENCODE v50→Rna Star→4 more tools
- Total tokens
- 98.8M
- Output
- 46.7K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
AnswerDEFB110
WorkflowFastqc→Salmon→Datamash Ops→Salmon quantification diagnostics→Rank human differential isoform usage→2 more tools
- Total tokens
- 7.9M
- Output
- 24.5K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
AnswerDEFB110
WorkflowSalmon→Converter Gz To Uncompressed→Tp Sort Header Tool→Grep→Isoform Switch Analysis→1 more tools
- Total tokens
- 23.5M
- Output
- 62.7K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectUDT + standard tools
AnswerDEFB110
WorkflowSalmon→Isoformswitchanalyzer→Isoform Switch Two Sample→Tp Head Tool
- Total tokens
- 8.6M
- Output
- 40.7K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectUDT + standard tools
AnswerDEFB110
WorkflowSalmon→Isoformswitchanalyzer→Isoform switch score→Filter Tabular
- Total tokens
- 25.3M
- Output
- 71.5K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
IncorrectUDT + standard tools
AnswerMS4A1
WorkflowSalmon→Upload1→Converter Gz To Uncompressed→Hisat2→Samtools Flagstat→9 more tools
- Total tokens
- 19.9M
- Output
- 70.8K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
AnswerDEFB110
WorkflowSalmon→Isoformswitchanalyzer→Two-sample isoform usage effect-size analysis→Supported two-sample isoform usage effect-size analysis→Cat1→5 more tools
- Total tokens
- 10.9M
- Output
- 68.2K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
AnswerDEFB110
WorkflowFastqc→Salmon→Converter Gz To Uncompressed→Kallisto Quant→GENCODE within-gene isoform usage comparison→2 more tools