User: deanna.church

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deanna.church1.1k
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Posts by deanna.church

<prev • 52 results • page 1 of 6 • next >
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Answer: A: Different position of the same alternative locus
... What NCBI produces is exactly what the GRC submit. Many other sources will re-align the alt-loci to the Primary assembly. We don't really treat alignments as a first class data object (no accession, versions, etc) so people feel free to do this. I think it just leads to confusion (as noted in the qu ...
written 21 months ago by deanna.church1.1k
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Comment: C: Hgvs Nomenclature Lookup?
... I actually no longer recommend using variation reporter. VEP, snpEff or Reece's hgvs package are easier to use and will give you better answers.  ...
written 2.9 years ago by deanna.church1.1k
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Answer: A: Reference genomes repository
... There is an assembly database at NCBI: www.ncbi.nlm.nih.gov/assembly This stores multiple assemblies per organism- though not all 'reference' quality.   ...
written 3.6 years ago by deanna.church1.1k
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Comment: C: Best/most common file format for CNV data
... I only showed a subset of the GVF file. I recommend looking at this- it works really well with array data (there is a lot of that in dbVar) and can cleanly handle the breakpoint ambiguity associated with arrays.  ...
written 3.9 years ago by deanna.church1.1k
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Answer: A: Best/most common file format for CNV data
... dbVar (http://www.ncbi.nlm.nih.gov/dbvar) and DGVa (http://www.ebi.ac.uk/dgva/) emit data as GVF as well: http://www.sequenceontology.org/resources/gvf.html ##gff-version 3 ##gvf-version 1.07 ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606 ##genome-build NCBI GRCh37.p13 ...
written 3.9 years ago by deanna.church1.1k
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Comment: C: Mapping Refseq Ng_ Regions To Chromosome Position
... Great! glad that was helpful.  ...
written 3.9 years ago by deanna.church1.1k
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Comment: C: Is It Possible To Perform De Novo Assembly Of Specific Regions Of Human Genome?
... Have you checked this against GRCh38 or just GRCh37? In general, regions not well covered in the reference are hard to assembly- but there is significant improvements in GRCh38 in the pericentromeric regions. ...
written 4.6 years ago by deanna.church1.1k
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Answer: A: Can Base Pair Positions Change Between Patches Of Builds? (Say Between Grch37.P5
... I'm not sure where you are getting your data- but here are some things to think about. 1. Assembly: The only difference between the patch releases (GRCh37.p*) and GRCh37 are the actual patch sequences. There are a few examples of patches that have updated between patch releases, but this is relative ...
written 4.6 years ago by deanna.church1.1k
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Answer: A: Why Are There Duplicate Refseq Entries Mapping To Identical Genome Locations?
... This looks like a bug at UCSC- if you view the RefSeq annotation you only see this once: http://tinyurl.com/ngpwts3 I'd recommend reporting this to UCSC to try to find out more. ...
written 4.6 years ago by deanna.church1.1k
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Comment: C: Grch38 And Reference Alignment
... I know of no variant callers that have been modified to handle this. sorry. :( ...
written 4.7 years ago by deanna.church1.1k

Latest awards to deanna.church

Scholar 8 months ago, created an answer that has been accepted. For A: Different position of the same alternative locus
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Is Human Chr17 Special In Any Way That We Have The Beginning And End Sequences F
Guru 20 months ago, received more than 100 upvotes.
Scholar 21 months ago, created an answer that has been accepted. For A: Different position of the same alternative locus
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Snp In A Haplotype Chromosome Block
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Snp In A Haplotype Chromosome Block
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Standalone Blast Issue
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Grch38 And Reference Alignment
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Will Grc38/Hg20 Be A Multiple Sequence Reference Genome?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Is Human Chr17 Special In Any Way That We Have The Beginning And End Sequences F
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: No Reads Ever Map To First 3Million Bases Of Chromosomes In Mouse Genome! Why?
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Will Grc38/Hg20 Be A Multiple Sequence Reference Genome?
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: Standalone Blast Issue
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: Applying Patches To Grch Assembly
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Grch38 And Reference Alignment
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Is Human Chr17 Special In Any Way That We Have The Beginning And End Sequences F
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Where Were The Human Genome Reference Samples Taken From?
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: No Reads Ever Map To First 3Million Bases Of Chromosomes In Mouse Genome! Why?
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Snp In A Haplotype Chromosome Block
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Will Grc38/Hg20 Be A Multiple Sequence Reference Genome?

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