Question
I have a single-cell ATAC-seq cluster counts pseudobulks lying around from human retinal-associated tissue (sample.swap.atac.q2.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. "AIIamacrine,Rod".
- Predicted answer
NoneMost likely answer for this question; not uniquely determined 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
Matches predictionUDT-only
AnswerNone
WorkflowDetect scATAC pseudobulk cell-type swap→Validate scATAC swap call across flanks
Codex GPT-5.5
Replicate 2
Matches predictionUDT-only
AnswerNone
WorkflowRetina ATAC profile diagnostic→Retina ATAC marker swap check→Retina ATAC marker window check
- Total tokens
- 645.4K
- Output
- 13.3K
Codex GPT-5.5
Replicate 3
Matches predictionUDT + standard tools
AnswerNone
WorkflowATAC pseudobulk diagnostic→ATAC pseudobulk diagnostic v2→UDT minimal copy→Grep→Bedtools Intersectbed→1 more tools
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
Matches predictionUDT-only
AnswerNone
WorkflowGalaxy UDT→swap_check→swap check→Retinal ATAC pseudobulk swap check→Retinal ATAC pseudobulk swap check corrected→1 more tools
- Total tokens
- 4.9M
- Output
- 18.9K
Codex GPT-5.6 Sol
Replicate 2
Matches predictionUDT-only
AnswerNone
WorkflowRetina pseudobulk marker accessibility diagnostic→Retina pseudobulk swap validation
- Total tokens
- 2.9M
- Output
- 14.9K
Codex GPT-5.6 Sol
Replicate 3
Matches predictionUDT-only
AnswerNone
WorkflowRetina swap marker diagnostic→Retina swap robust validation
- Total tokens
- 1.2M
- Output
- 12.2K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
Matches predictionStandard tools only
AnswerNone
WorkflowTp Cut Tool→Bedtools Intersectbed→Bedops Sort Bed→Tp Tail Tool→Bedtools Sortbed→6 more tools
- Total tokens
- 18.7M
- Output
- 65.8K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Matches predictionUDT + standard tools
AnswerNone
WorkflowDatamash Ops→ATAC pseudobulk stats→ATAC marker accessibility scores→ATAC marker accessibility scores v2→Network probe→1 more tools
- Total tokens
- 5.5M
- Output
- 37.3K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Matches predictionUDT-only
AnswerNone
WorkflowRetina ATAC sample swap check→Retina ATAC sample swap check v2
- Total tokens
- 3.7M
- Output
- 46.3K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
Matches predictionUDT + standard tools
AnswerNone
WorkflowSummary Statistics1→Retinal ATAC column diagnostic→Retinal ATAC UDT runtime probe→Retinal Atac Direct Build Probe4→Select columns→5 more tools
- Total tokens
- 23.8M
- Output
- 84.8K
Codex GPT-5.6 Luna
Replicate 2
Matches predictionUDT-only
AnswerNone
WorkflowATAC swap diagnostic→ATAC marker locus probe→ATAC holdout marker assignment→ATAC marker assignment validation
- Total tokens
- 2.0M
- Output
- 33.4K
Codex GPT-5.6 Luna
Replicate 3
Matches predictionUDT-only
AnswerNone
WorkflowATAC Profile Diagnostic→ATAC Marker Locus Probe→ATAC Build and Marker Comparison→ATAC Sample Swap Check
- Total tokens
- 3.5M
- Output
- 32.2K