User: arronslacey

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arronslacey220
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Posts by arronslacey

<prev • 79 results • page 1 of 8 • next >
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Convert SNPs from GrCh38 to 37
... The following SNPs are from the GRCh38 build 1 158766655 158766655 C T 1 162023402 162023402 T C 1 169793666 169793666 T G 1 6554475 6554475 G A 3 179604597 179604597 A C 4 39062542 39062542 A C 5 177089630 177089630 G A 8 142786489 142786489 C T 8 142879785 1428 ...
grch37 grch38 mapping snp written 9 weeks ago by arronslacey220 • updated 9 weeks ago by harold.smith.tarheel3.9k
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Comment: C: merging humsavar dataset with UniprotKB human variation
... Hi @emmahe - Although the chromosome number and chromosome position are given in the annotation track bed file, the nucleotide allele change is not present. I perhaps should have explained this a bit better. Thanks. ...
written 12 weeks ago by arronslacey220
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merging humsavar dataset with UniprotKB human variation
... Hi - in the current release ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants I am interested in putting all variants annotated within humsavar.txt through Annovar or other annotation tools. Perhaps even score them with something like CADD. I require all the varian ...
ensembl swissprot uniprot snp annovar written 12 weeks ago by arronslacey220 • updated 12 weeks ago by emmahe40
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drug response variant datasets
... Hi - I am looking for sources of drug response data at SNP level for data mining purposes in my Phd. I m aware of Biobase's PGMD which looks promising, however I don't have the 12k euros for the download subscription for raw access! I'd be very grateful of anyone knows of any alternative databases. ...
snp variant drug response biobase written 14 months ago by arronslacey220 • updated 12 months ago by dyollluap280
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Comment: C: chromosomal locations of snps in humvar variant set
... Thanks Elisabeth - very helpful! I had also looked into the Bisoconductor package VariantAnnotation that includes data objects such as polyPhen.Hsapiens.dbSNP131 - which maps most of the rsids to the humsavar dataset. it's obviously a bit out of date now so I much appreciate alternative data scourse ...
written 19 months ago by arronslacey220
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chromosomal locations of snps in humvar variant set
... Hi - in the humsavar dataset there are variants given by protein position and amino acid change. http://www.uniprot.org/docs/humsavar Is there a way to convert these to chromosome positions and nucleotide changes? thanks. I should probably add for clarification that some snps listed to do not hav ...
variation humvar snp uniprot written 19 months ago by arronslacey220 • updated 19 months ago by Elisabeth Gasteiger1.2k
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how can I obtain benign / neutral snps?
... Hi everyone - using the UCSC server it seems I can obtain disease causing SNPs from snp144 by doing something like select * from snp144 where bitfields like '%has-omim-omia%' but I would like to know if there is a preferred way to select non-disease causing snps. i.e. known to be benign. Is th ...
annovar dbnfsp snp mysql dbsnp written 19 months ago by arronslacey220 • updated 19 months ago by WouterDeCoster23k
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Comment: C: Multiple annotations using annovar?
... just one thing - table_annovar.pl does not seem to preserve additional custom fields specified in the input file, where annotate_variation.pl appears to do this. do you happen to know how to keep extra columns in the input? all my additional columns are in the format comments: field1 field ...
written 20 months ago by arronslacey220
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Comment: C: Multiple annotations using annovar?
... excellent thanks very much! ...
written 20 months ago by arronslacey220
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Multiple annotations using annovar?
... Hi - is it possible to add multiple annotations in the same command with annovar. For example annotation with both exac and 1000g? The command for one is this: perl annotate_variation.pl -filter -build hg19 -dbtype exac03 GLRA1.txt humandb/ so I have tried perl annotate_variation.pl -f ...
annovar variant annotation written 20 months ago by arronslacey220 • updated 20 months ago by igor4.7k

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