User: Tao

gravatar for Tao
Tao420
Reputation:
420
Status:
Trusted
Location:
Last seen:
4 months, 3 weeks ago
Joined:
7 years, 6 months ago
Email:
w***************@gmail.com

about me

Posts by Tao

<prev • 77 results • page 1 of 8 • next >
0
votes
1
answer
165
views
1
answers
Comment: C: Plink with hwe option does not work
... NO worries. Please upvote or accept my post if you think useful :) ...
written 5 months ago by Tao420
0
votes
1
answer
165
views
1
answers
Answer: A: Plink with hwe option does not work
... There is incompatibility between options in PLINK. I would suggest you to separate your process into two steps: --hwe, --maf are for quality control; and --chr --from-bp --to-bp are for extracting. And --out should be prefix names of output plink files, not folder name. ...
written 5 months ago by Tao420
0
votes
2
answers
143
views
2
answers
Answer: A: color gradient for heatmap2
... I think you can try to remove col=bluered(100), because in default, they use yellow-red schema. P.S. You can create a vector of n contiguous colors using the functions rainbow(n), heat.colors(n), terrain.colors(n), topo.colors(n), and cm.colors(n). ...
written 5 months ago by Tao420
0
votes
0
answers
191
views
0
answers
Comment: C: How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
... Hi, I think reference allele refers to the allele shown in the reference genome, isn't it? Please check the website: https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation/what-are-variants-alleles ...
written 5 months ago by Tao420
0
votes
0
answers
191
views
0
answers
Comment: C: How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
... That is definitely a possible way. Thanks Pierre. But if ref allele is small indel, that could be a problem. ...
written 5 months ago by Tao420
0
votes
0
answers
191
views
0
answers
How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
... Given the chromosome, position and A1 allele, A2 allele, how to easily tell which allele is the reference allele? I know it is possible to extract the annotation from dbSNP, 1000G or other reference panels. But, that will need to download large mount of data. What I am looking are more efficient w ...
ref allele reference allele snp written 5 months ago by Tao420
0
votes
1
answer
288
views
1
answers
Comment: C: Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
... Thanks for your prompt and deep insights! ...
written 11 months ago by Tao420
0
votes
1
answer
288
views
1
answers
Comment: C: Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
... Thanks for your comments. But I am not quite understand that why plink doesn't directly count the real haplotypes from samples? since the 1000G genotypes are phased. ...
written 11 months ago by Tao420
2
votes
1
answer
288
views
1
answer
Inspect the LD relation between a single pair of SNPs in detail using Plink --ld
... When I calculate the LD details between a pair of SNPs using following command as an example, why there might be two solutions shown as following (Q1)? plink --bfile 1000G.genotypes --ld rs10005588 rs12505231 > Solution #1: R-sq = 0.000943758 D' = 1 Haplotype ...
--ld plink ld written 11 months ago by Tao420 • updated 11 months ago by chrchang5237.3k
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Recoding bim to vcf file with forcing allele-A1
... Hi, I got the same problem. That is because when you were converting plink to vcf, probably using plink --recode vcf, "The A2 allele is saved as the reference and normally flagged as not based on a real reference genome ('PR' INFO field value)." See plink explanation [here][1]. That's saying the --r ...
written 16 months ago by Tao420

Latest awards to Tao

Great Question 11 months ago, created a question with more than 5,000 views. For Extract data using awk/sed and output to different files
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How to efficiently remove a list of reads from BAM file?
Great Question 16 months ago, created a question with more than 5,000 views. For How to efficiently remove a list of reads from BAM file?
Scholar 17 months ago, created an answer that has been accepted. For A: WGCNA signed vs unsigned network
Popular Question 19 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 19 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Great Question 21 months ago, created a question with more than 5,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 21 months ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Should I use reads with good quality but failed-vendor flag?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Scholar 2.9 years ago, created an answer that has been accepted. For A: How to choose NCBI viral database?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: WGCNA signed vs unsigned network
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Extract data using awk/sed and output to different files
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How to efficiently remove a list of reads from BAM file?
Supporter 4.3 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 998 users visited in the last hour