User: Jie Ping

gravatar for Jie Ping
Jie Ping20
Reputation:
20
Status:
New User
Location:
China
Last seen:
8 months ago
Joined:
4 years, 8 months ago
Email:
j*******@foxmail.com

Posts by Jie Ping

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Identifying mutations between haplotypes using haploNet (pegas) in R
... Yes! We can get the sequence of each haplotype by using function `diffHaplo` in R package `pegas`. ## For example, ### 1. generate test data > data(woodmouse) > x <- woodmouse[sample(15, size = 110, replace = TRUE),] > h <- haplotype(x) > (net <- haploNet(h)) Haplot ...
written 9 months ago by Jie Ping20
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Comment: A: Why might ancestral allele states in 1000G be wrong?
... It makes me confused. And, how could we annotate the right ancestral allele for vcf file? ...
written 10 months ago by Jie Ping20
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Comment: C: Why no SNPs are at chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array
... Yes! I agree with you. Well, I still want to confirm whether some other reason exists, cause I am doing some job in this region. What would you suggest me to do to figure it out? ...
written 2.1 years ago by Jie Ping20
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Comment: C: Why no SNPs are at chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array
... Thank you for reply. You are correct. I also noted that Affy 6.0 do not have genomic position based on hg19. But for the purpose of keeping the consistent positions with my whole genome seq data, I turned positions to build hg19 using liftover from UCSC browser. I am wondering that whether SNPs at ...
written 2.1 years ago by Jie Ping20
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Why no SNPs are at chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array
... Perhaps many regions in human genome are absent in Affy 6.0 array due to the limited sampling in human genome. However, I want to know why no SNPs are at exact chr6:13650971-13954632 (based on hg19) in Affy 6.0 snp array? Could anyone help? Best regards, ...
genome snp array snp written 2.1 years ago by Jie Ping20 • updated 14 months ago by Biostar ♦♦ 20
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Exact FDR value of DEPICT software?
... Hello, everyone! I use DEPICT([link here][1]) for tissue/cell type enrichment analysis. BUT the output file named "_tissueenrichment.txt" DOES show "YES/NO" of FDR column instead of the exact FDR value. And another question is what the genes enrich in the significant tissue? Does anyone help me w ...
software error snp written 2.7 years ago by Jie Ping20 • updated 2.7 years ago by Biostar ♦♦ 20
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Which city of China are CHS at 1000genomes from?
... For getting a control population to high altitude adaptation, actually I want to know the altitude of the city where CHS population come from. I did not get informations about altitude at http://www.1000genomes.org/home. That is the question. Thanks in advance! ...
genome written 4.1 years ago by Jie Ping20 • updated 4.1 years ago by kautilya380
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Comment: C: How to prioritize regions under positive selection
... The mission is to find out genes under selection. But I found there were too many genes significant in at least one test...What do you recommend, such as some experience or papers? ...
written 4.3 years ago by Jie Ping20
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How to prioritize regions under positive selection
... After tesets of selection on WGS data, there would be a lot of regions as significant in at least one test under the correspongding 0.1% genome-wide FDR. And my question is: How to prioritize regions for the subsequent research? ...
evolution sequencing written 4.4 years ago by Jie Ping20 • updated 4.3 years ago by Giovanni M Dall'Olio26k
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Answer: A: How to get ancestral SNPs states for GRCh37.p13
... You can find 1kg ancestral alleles (actually derived from Ensembl) here.     ...
written 4.4 years ago by Jie Ping20

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to get unphased VCF file phased by shapeit?

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