User: janhuang.cn

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janhuang.cn120
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Posts by janhuang.cn

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Illumina Human Methylation EPIC array annotation
... Thanks. The column heading says "UCSC_RefGene_Name: Target gene name(s), from the UCSC database. *Note: multiple listings of the same gene name indicate splice variants". But is there any information on how they (UCSC or Illumina) annotate it? For example, cg18478105 (chr20:61847650) was on YTHDF1 ( ...
written 5 weeks ago by janhuang.cn120
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Illumina Human Methylation EPIC array annotation
... I used the R package *IlluminaHumanMethylationEPICanno.ilm10b4.hg19* to extract the annotation of the CpGs in my data. I wonder if there is any documentation on how Illumina define these annotations? Is it solely based on the distance from the loci? Thank you very much. ...
dna methylation epic array annotation written 5 weeks ago by janhuang.cn120 • updated 5 weeks ago by Charles Warden5.9k
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Comment: C: Infinium Methylation SNP
... Thank you very much ...
written 15 months ago by janhuang.cn120
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Comment: C: Infinium Methylation SNP
... How is full capture sequence defined? ...
written 15 months ago by janhuang.cn120
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Infinium Methylation SNP
... I am using `IlluminaHumanMethylation450kanno.ilmn12.hg19` package to obtain the SNP-associated probe information (probe_rs, probe_maf). The [reference manual][1] says > In addition to the SNP information provided by Illumina, we have added independent information on the overlap of the 450k wit ...
overlap snp cpg written 15 months ago by janhuang.cn120 • updated 15 months ago by andrew.j.skelton735.5k
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Comment: C: SNPs that are merged in dbSNP
... Using the "Send to" function to download is very slow. RsMergeArch.bcp.gz is available in the dbSNP FTP folder: [ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/ ...
written 15 months ago by janhuang.cn120
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Comment: C: Downloading synonyms for dbSNP rsids
... The above link is expired. The RsMergeArch.bcp.gz is now available here: [ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/ ...
written 15 months ago by janhuang.cn120
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Comment: C: SNPs that are merged in dbSNP
... Thank you very much. ...
written 15 months ago by janhuang.cn120
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SNPs that are merged in dbSNP
... I am analysing the 1000G VCF files, rs80314515 is not available in the VCF, but rs10204648 is available. dbSNP returns this message when I search rs80314515 ([https://www.ncbi.nlm.nih.gov/snp/?term=rs80314515][1]) rs80314515 has merged into rs10204648 I wonder if there is a data base about ...
1000g vcf merge snp written 15 months ago by janhuang.cn120 • updated 15 months ago by Kevin Blighe35k
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Comment: C: Extract the SNP list of a VCF file
... Thank you very much. ...
written 15 months ago by janhuang.cn120

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Popular Question 14 months ago, created a question with more than 1,000 views. For Fail to open file in plink
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