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How I learne d to quit worrying

How I learne d to quit worrying. And love multiple coordinate systems. Deanna M. Church Staff Scientist, NCBI. Short Course in Medical Genetics 2013. @ deannachurch. Alternate loci/Patch. Transcripts (NM_XXXXXX.X). Proteins (NP_XXXXXX.X). RefSeqGene /LRG. * Not drawn to scale.

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How I learne d to quit worrying

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  1. How I learned to quit worrying And love multiple coordinate systems Deanna M. Church Staff Scientist, NCBI Short Course in Medical Genetics 2013 @deannachurch

  2. Alternate loci/Patch Transcripts (NM_XXXXXX.X) Proteins (NP_XXXXXX.X) RefSeqGene/LRG * Not drawn to scale

  3. http://www.ncbi.nlm.nih.gov/genome/tools/remap

  4. Software v1.4 Different versions of same assembly to each other (e.g. NCBI36<->GRCh37) Different assemblies from same organism to each other (HuRef<->GRCh37)

  5. Producing Assembly-Assembly Alignments First Pass Alignments: Symmetrical best hits- only 0 or 1 alignment to the other assembly. Second Pass Alignments: attempt to recover regions not in the first pass Uses assembly structure to guide first pass alignments

  6. NCBI36 Remap failure: low coverage (<50%) GRCh37 100 bp NCBI36 Remap failure: expansion (target length/source length >2) 400 bp GRCh37

  7. Helps rescue features that cross a gap (common for CNVs/Structural Variants)

  8. Beware: Second Pass alignments and Merge

  9. Remap Output Summary data: Quick overview of how well your features mapped Mapping report: Detailed report containing all of your input featuresand their source location, target location (or reason for failure) and coverage score. Annotation File: An annotation file of only the features that successfullyremapped. Suitable for loading to most browsers. Genome Workbench file: A file formatted for loading to Genome Workbench (a client side browser). Includes assembly-assembly alignments forreview. Genome Workbench videos

  10. * LRG soon When mapping to RefSeqGene Genomic location (NG_XXXXXX.X) Transcript location(s) (NM_XXXXXX.X) Protein location(s) (NP_XXXXXX.X) Optional, but checkedby default No second pass alignments, only one ‘best’ alignment

  11. Maps features: From Primary Assembly -> Alternate Loci/Patches (common) From Alternate Loci/Patches->Primary Assembly No second pass alignments, only one ‘best’ alignment

  12. Take home messages • Tools are available for mapping features from onecoordinate system to another. • Assembly <-> Assembly • Assembly <-> RefSeqGene • Primary Assembly <-> Alternate Loci/Patches • Feature remapping is NOT a substitute for de novo annotation.

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