User: janhuang.cn
janhuang.cn • 150
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Posts by janhuang.cn
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... But I got the similar error message no matter I put .gz or not.
plink --vcf ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --r2 --ld-window-r2 0.8 --ld-snp rs157595
Error: Failed to open
ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes ...
written 11 months ago by
janhuang.cn • 150
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... Error: Failed to open
ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.
I got an error when using --vcf for gzipped vcf
...
written 11 months ago by
janhuang.cn • 150
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... I would like to find the proxy SNPs (r2>0.8) for a list of SNPs. I have a long list, so I do not want to manually check and download from LDlink. I think plink and/or vcftools can do the job. But I came across some problems.
I download the 1000G phase3 vcf (gzziped) from the ftp folder: [ftp://f ...
written 11 months ago by
janhuang.cn • 150
• updated
11 months ago by
chrchang523 ♦ 6.5k
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... 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 14 months ago by
janhuang.cn • 150
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...
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.
...
written 14 months ago by
janhuang.cn • 150
• updated
14 months ago by
Charles Warden ♦ 7.6k
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Comment:
C: Infinium Methylation SNP
... Thank you very much
...
written 2.3 years ago by
janhuang.cn • 150
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Comment:
C: Infinium Methylation SNP
... How is full capture sequence defined? ...
written 2.3 years ago by
janhuang.cn • 150
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... 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 ...
written 2.3 years ago by
janhuang.cn • 150
• updated
2.3 years ago by
andrew.j.skelton73 ♦ 5.9k
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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 2.4 years ago by
janhuang.cn • 150
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... 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 2.4 years ago by
janhuang.cn • 150
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