Question
I have a scRNA-seq pseudobulk lying around from amphioxus tissue (sample.swap.rna.q1.tsv.gz). I'm not sure, but I suspect there is a sample swap. Can you check if that is the case? If there isn't, respond "None". Else respond with the names of the two cell types that have been swapped in case-sensitive lexicographic order, e.g. "endoderm,epidermis".
- Inferred answer
epidermal_neural,tailbud_neuralUniquely inferred from submitted scores.- Domain
- Single-cell
- Question style
- Metadata Recovery
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-only
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus Reference Layout Probe→Detect Amphioxus Pseudobulk Sample Swap→Summarize Amphioxus Reference Labels→Detect Amphioxus Pseudobulk Sample Swap v2→Detect Amphioxus Swap From Single Cell Counts→3 more tools
Codex GPT-5.5
Replicate 2
CorrectUDT-only
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus swap check→Amphioxus swap check v2→Amphioxus swap check v3
- Total tokens
- 3.2M
- Output
- 13.6K
Codex GPT-5.5
Replicate 3
RerunIncorrectUDT + standard tools
AnswerNone
WorkflowSelect first→Swap diagnostic for pseudobulk matrix→Annotate BLAG marker genes from BraLan3 GFF→Extract selected marker expression from pseudobulk
- Total tokens
- 2.4M
- Output
- 18.2K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectUDT-only
Answerepidermal_neural,tailbud_neural
WorkflowPseudobulk geometry and specificity→Inspect BLAG annotation overlap→Summarize amphioxus cell annotations→Reconstruct and match amphioxus pseudobulk→Summarize pseudobulk assignment→1 more tools
- Total tokens
- 36.5M
- Output
- 28.6K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT-only
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus pseudobulk annotation diagnostic→Amphioxus pseudobulk swap reference match
- Total tokens
- 4.0M
- Output
- 15.8K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT-only
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus pseudobulk profile diagnostic→Amphioxus authoritative reference swap test→Amphioxus authoritative fine reference swap test→Amphioxus exhaustive 12-profile swap validation
- Total tokens
- 8.4M
- Output
- 16.7K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
Answerepidermal_neural,tailbud_neural
WorkflowNo Galaxy tool job recorded
- Total tokens
- 49.9M
- Output
- 135.6K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectUDT-only
Answerepidermal_neural,tailbud_neural
WorkflowSample Swap Compare→Sample Swap Compare v2
- Total tokens
- 1.4M
- Output
- 17.4K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectUDT + standard tools
Answerepidermal_neural,tailbud_neural
WorkflowCheck Pseudobulk Sample Swap→UDT Probe→UDT Probe Busybox→Datamash Transpose→Table Compute→10 more tools
- Total tokens
- 38.6M
- Output
- 147.1K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
CorrectUDT + standard tools
Answerepidermal_neural,tailbud_neural
WorkflowGroup and aggregate→Tp Head Tool→Amphioxus source matching diagnostic→UDT render probe→UDT exact documentation probe→18 more tools
- Total tokens
- 63.5M
- Output
- 140.5K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus swap diagnostic→UDT render probe→UDT input render probe→UDT command probe→UDT legacy probe→18 more tools
- Total tokens
- 48.5M
- Output
- 138.0K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
Answerepidermal_neural,tailbud_neural
WorkflowAmphioxus sample swap diagnostic→UDT copy probe→UDT shell probe→Tp Head Tool→UDT resource probe→19 more tools
- Total tokens
- 70.3M
- Output
- 182.8K