User: jxchong

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jxchong160
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160
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Postdoc at the University of Washington
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Last seen:
4 years, 7 months ago
Joined:
6 years, 6 months ago
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Postdoc in the Bamshad lab at the University of Washington. Former grad student in the Ober lab at the University of Chicago.

Posts by jxchong

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Ranking And Prioritizing Non-Coding Variants
... Determining functionality (or lack thereof) of non-coding variants is an open area of research, so finding a ranking/prediction algorithm similar to Polyphen/SIFT is probably unlikely at this point in time. You can check out GREAT: http://bejerano.stanford.edu/great/public/html/index.php ...
written 5.7 years ago by jxchong160
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Answer: A: Transcripts - Coding Or Ncrna ?
... Those are all Ensembl transcript IDs. You can look up all the information about them on Ensembl Genome Browser. Example: http://uswest.ensembl.org/Homo_sapiens/Search/Details?db=core;end=1;idx=Gene;q=ENST00000492842;species=Homo_sapiens ...
written 5.9 years ago by jxchong160
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Comment: C: Annotate Regions In Bed File With Nearest Downstream Gene
... Since TSSE has no strand info, it could be acting on either the + or - strand? TSSE is upstream of geneE on the - strand and upstream of geneF on the + strand, but it is closer to geneE on the - strand than it is to geneF on the + strand. ...
written 6.0 years ago by jxchong160
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Comment: C: Annotate Regions In Bed File With Nearest Downstream Gene
... Oops, fixed now. (I'll need to add "chr" in, run bedops, strip out chr later so I can combine the data with my vcf) :P But... that's a separate issue. ...
written 6.0 years ago by jxchong160
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Comment: C: Annotate Regions In Bed File With Nearest Downstream Gene
... Hmm, I had looked into closest-features, but this method won't work on: TSS.bed chr3 3 4 TSSE genes.bed chr3 1 2 geneE 0 - chr3 21 22 geneF 0 + The result associates TSSE with geneF (instead of geneE, as desired). However, I think by combining Istv ...
written 6.0 years ago by jxchong160
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Comment: C: Annotate Regions In Bed File With Nearest Downstream Gene
... Thanks, but no, that isn't what I want to do -- I don't want to detect the TSS for a given gene, I want to annotate all TSS with their nearest gene (because these are computational predictions, sometimes there are multiple separated TSS regions that are all clearly for the same gene. Additionally a ...
written 6.0 years ago by jxchong160
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Annotate Regions In Bed File With Nearest Downstream Gene
... I have a bed file with predicted TSS/promoter regions (by chromHMM and similar methods) and I would like to annotate each region from the bed file with the gene(s) it is likely to act upon. I could use closestBed (bedtools) to get the closest genes purely by genomic distance, but it seems like I ...
bed promoter written 6.0 years ago by jxchong160 • updated 5.0 years ago by Biostar ♦♦ 20
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Answer: A: Extracting Gene Names From Vcf File
... vcftools vcf-query http://vcftools.sourceforge.net/perl_module.html#vcf-query Have it output %txGN or %INFO/txGN depending on where txGN is stored ...
written 6.3 years ago by jxchong160
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Answer: A: Nomenclature For Alleles
... Hmm, actually it depends on where you got that nucleotide change and who was writing it. The G could be any of these things: 1) ancestral allele 2) reference genome allele 3) major allele. These three things are not necessarily the same allele at a given position! ...
written 6.4 years ago by jxchong160
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Answer: A: Simple Question About .Ped Format For Gatk And Plink
... the delimiter is spaces or tabs. This link will help: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped In particular: The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory: Family ID Individual ID Paternal ID Maternal ID Sex (1=male; 2=fe ...
written 6.4 years ago by jxchong160

Latest awards to jxchong

Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Ranking And Prioritizing Non-Coding Variants
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Ranking And Prioritizing Non-Coding Variants
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Annotate Regions In Bed File With Nearest Downstream Gene
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Simple Question About .Ped Format For Gatk And Plink
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Ranking And Prioritizing Non-Coding Variants
Autobiographer 5.7 years ago, has more than 80 characters in the information field of the user's profile.

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