Codex GPT-5.5
Replicate 1
IncorrectUDT-only
Answer
2;-2Workflow
Fragment summary diagnosticTn5 shift chr1 diagnosticTn5 shift multichrom final
- Total tokens
- 525.8K
- Output
- 11.0K
Question
I got a scATAC-seq fragment file (unknown.shift.frag.bed.gz) from a colleague who aligned it to the hg38 genome. However, they applied a non-standard shift to the reads instead of the typical +4/-5. Can you help figure out what it is? Report answer in the format "3;-3" (corresponding to values for 5' and 3' ends).
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 resultsUDT = 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 replicatesCodex GPT-5.5
Replicate 2
CorrectUDT-only
Answer
2;-1Workflow
ATAC shift diagnosticATAC shift diagnostic v2UDT smoke copy
- Total tokens
- 1.8M
- Output
- 19.1K
Codex GPT-5.5
Replicate 3
RerunIncorrectUDT-only
Answer
6;-5Workflow
ATAC shift endpoint sequence diagnosticATAC shift candidate scorerATAC shift HINT bias validationATAC shift HINT native kmer validation
- Total tokens
- 1.7M
- Output
- 24.6K
Codex GPT-5.6 Sol
3 replicatesCodex GPT-5.6 Sol
Replicate 1
CorrectUDT + standard tools
Answer
2;-1Workflow
Extract Genomic Dna 1Infer Tn5 shift from fragment-end sequence biasCreate centered fragment-end windowsCreate left fragment-end windowsLocate Tn5 bias axis in centered endpoint windows1 more tools
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
Answer
2;-1Workflow
Make oriented endpoint windowsExtract Genomic Dna 1Analyze endpoint sequence biasCall nonstandard Tn5 shift
- Total tokens
- 914.3K
- Output
- 11.0K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
Answer
2;-1Workflow
Bedtools SlopbedExtract Genomic Dna 1Infer Tn5 fragment endpoint shifts
- Total tokens
- 2.9M
- Output
- 14.1K
Codex + DeepSeek-v4-pro-0813
3 replicatesCodex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
Answer
2;-1Workflow
Add A Column1Converter Gz To UncompressedSelect columnsBedtools GetfastabedFasta Nucleotide Color Plot2 more tools
- Total tokens
- 26.2M
- Output
- 95.9K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectUDT + standard tools
Answer
2;-1Workflow
No Galaxy tool job recorded
- Total tokens
- 4.6M
- Output
- 38.6K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectUDT + standard tools
Answer
2;-1Workflow
Make ATAC endpoint pointsGet Flanks1Extract Genomic Dna 1Converter Interval To Bed 0Bedtools Getfastabed19 more tools
- Total tokens
- 57.0M
- Output
- 256.6K
Codex GPT-5.6 Luna
3 replicatesCodex GPT-5.6 Luna
Replicate 1
RerunCorrectUDT + standard tools
Answer
2;-1Workflow
Add a column1 → User-defined tool → datamash ops → Count1 → bedtools getfastabed → seq composition → fasta2tab
- Total tokens
- 27.2M
- Output
- 98.4K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
Answer
2;-1Workflow
Fragment basic diagnosticUDT rendering probeUDT rendering probe v2UDT rendering probe v3UDT rendering probe v421 more tools
- Total tokens
- 24.4M
- Output
- 77.7K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
Answer
2;-1Workflow
Fragment Structure DiagnosticExtract hg38 TSS BEDTSS Shift ProbeTSS Coverage Shift GridFragment Preview7 more tools
- Total tokens
- 19.2M
- Output
- 78.0K
Anycode
13/13 terminal item resultsCodex GPT-5.5
3 replicatesCodex GPT-5.5
Replicate 1
Incorrect
Answer
3;-3Workflow
Local codePython
Codex GPT-5.5
Replicate 2
Correct
Answer
2;-1Workflow
Local codePython
Codex GPT-5.5
Replicate 3
Incorrect
Answer
2;-2Workflow
Local codeSamtoolsBedtoolsPython
Codex GPT-5.6 Sol
3 replicatesCodex GPT-5.6 Sol
Replicate 1
Correct
Answer
2;-1Workflow
Local codePython
Codex GPT-5.6 Sol
Replicate 2
Correct
Answer
2;-1Workflow
Local codePython
Codex GPT-5.6 Sol
Replicate 3
Correct
Answer
2;-1Workflow
Local codePython
Codex + DeepSeek-v4-pro-0813
3 replicatesCodex + DeepSeek-v4-pro-0813
Replicate 1
Incorrect
Answer
6;-6Workflow
Local codeSamtoolsBedtoolsPythonSciPy
- Total tokens
- 2.7M
- Output
- 40.3K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Correct
Answer
2;-1Workflow
Local codeSamtoolsBedtoolsPythonpysam1 more tools
- Total tokens
- 3.5M
- Output
- 42.1K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Correct
Answer
2;-1Workflow
Local codePythonpysam
- Total tokens
- 3.3M
- Output
- 38.8K
Codex GPT-5.6 Luna
3 replicatesCodex GPT-5.6 Luna
Replicate 1
Correct
Answer
2;-1Workflow
Local codeSamtoolsBedtoolsPythonpysam
Codex GPT-5.6 Luna
Replicate 2
Correct
Answer
2;-1Workflow
Local codePythonSamtoolspysamSciPy1 more tools
Codex GPT-5.6 Luna
Replicate 3
Incorrect
Answer
2;-9Workflow
Local codeSamtoolsBedtoolsPython
Codex GPT-6 Astra
1 replicateCodex GPT-6 Astra
Replicate 1
Correct
Answer
2;-1Workflow
Local codePythonSamtools
- Total tokens
- 108.5K
- Output
- 1.6K