User: star

gravatar for star
star190
Reputation:
190
Status:
Trusted
Location:
Netherlands
Last seen:
12 hours ago
Joined:
3 years, 11 months ago
Email:
s***************@gmail.com

Posts by star

<prev • 162 results • page 1 of 17 • next >
1
vote
1
answer
75
views
1
answer
How extract data from gnomAD for some genes?
... I like to extract variant details about some genes from gnomAD 'https://gnomad.broadinstitute.org/', but I don`t want to do it by hand. I would like to know, is there any way to extract it by command line for below genes? Table A: RFPL3 RGMA RGS11 RHOT1 RIPOR1 RIPOR3 R ...
data gnomad variants written 3 days ago by star190
0
votes
1
answer
85
views
1
answer
How draw Phylogeny tree using genotype file?
... I like to draw a phylogenetic tree for some samples based on SNP regions and genotype for each sample, I used 'SNPhylo' but it couldn`t help me because I only have 90 SNP regions and I got error based on 'SNPhylo'. I would like to know is there any way to draw a nice tree based on the data that I ha ...
phylogenic_tree R tree phylogenetic written 15 days ago by star190 • updated 15 days ago by YJ0
0
votes
0
answers
72
views
0
answers
Change color using colRow only for some rows in heatmap?
... I draw a heatmap using below command: but I want to color some rows in a different color (like red) in the heatmap e.g. only `ABCB5` and `MAD1L1` Data: gene.ID name A B ENSG00000002822 MAD1L1 0.00 0.01818182 ENSG00000007264 MATK 1.00 0.00000000 ENSG00000004846 ...
R heatmap written 17 days ago by star190
3
votes
1
answer
93
views
1
answer
Not call some variants in some populations?
... I have three VCF files from three populations where I merged all their SNPs together. For some variants, there are genotypes in all population but not for all regions, so I got 'NA', I like to know what does it mean? means: no variant call for this region in samples with 'NA' or can I consider 'NA' ...
vcf variantion written 4 weeks ago by star190 • updated 4 weeks ago by bari.ballew190
0
votes
0
answers
171
views
0
answers
Comment: C: why there is 0/0 genotyp in VCF file?
... We don`t get ./. genotype, if there is low Q mapping? ...
written 5 weeks ago by star190
0
votes
0
answers
171
views
0
answers
Comment: C: why there is 0/0 genotyp in VCF file?
... I guess it is only one sample. here is the header of VCF: ##GATKCommandLine.HaplotypeCaller= ...
written 5 weeks ago by star190
0
votes
0
answers
171
views
0
answers
Comment: C: why there is 0/0 genotyp in VCF file?
... Thanks but my VCF is a single sample VCF file. ...
written 5 weeks ago by star190
9
votes
0
answers
171
views
0
answers
why there is 0/0 genotyp in VCF file?
... I have multiple VCF files (they are not multiple-sample VCF) and I just looked the genotypes and I saw there are 4 genotypes for each variant like: 0/0, 0/1, 1/1, ./. . The last three genotypes are clear to me, but I don`t understand why we have 'Hom_ref genotype' in the VCF files? And shall I ignor ...
vcf gatk variant written 5 weeks ago by star190
1
vote
2
answers
153
views
2
answers
How to remove all characters after a specific pattern?
... I have a big table like 'df', I would like to remove all value after first ':' for each row. I have tried : `cat df.bed | cut -f1 -d":" | head` and `cat df.bed |sed 's/:.*//' | head` but they removed all columns after first ':' . df: rs1006501 T A 0/0:14,0:14:42:0,42,596 A 0/0:5,0:5:15: ...
linux sed rna-seq awk written 5 weeks ago by star190 • updated 5 weeks ago by Jeffin Rockey1.1k
0
votes
1
answer
207
views
1
answers
Comment: C: select rows with specific columns and values between two data tables ?
... I have tried with If else but, I do not know how to select first and the last match for 1 and -1 value or the coordinates after and before them. It the cod that I have tried but it is not what I want: if (A$V6 %in% B$V1 & B$V3 == '1') { A[which(A$V4 == B$V4),] & A[which(A$V4 < ...
written 6 weeks ago by star190

Latest awards to star

Popular Question 14 days ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 21 days ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 4 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 4 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 6 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Voter 6 months ago, voted more than 100 times.
Centurion 7 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?
Popular Question 13 months ago, created a question with more than 1,000 views. For How can get MAF for set of SNPs from each population based on 1000 Genome?
Supporter 15 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For How can get MAF for set of SNPs from each population based on 1000 Genome?
Popular Question 18 months ago, created a question with more than 1,000 views. For How convert q-value to p-value?
Popular Question 19 months ago, created a question with more than 1,000 views. For How convert q-value to p-value?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How convert q-value to p-value?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Why most of alternative alleles are the alleles with major frequency?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1622 users visited in the last hour