Latest
News
Jobs
Tutorials
Forum
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
861 results • Page
1 of 18
Sort: Rank
Rank
Views
Votes
Replies
Filtering for tag:
gwas
•
reset
1
vote
0
replies
35
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS
power
19 hours ago by
moxu
▴ 480
0
votes
1
reply
51
views
LDSC -Genetic correlation, some results all have NA valuies
correlation
ldsc
genetic
gwas
updated 1 day ago by
Sam
★ 3.4k • written 1 day ago by
d.s.zimmerman
• 0
0
votes
1
reply
72
views
Create a phenotype file in PLINK format
gwas
phenotype
plink
updated 5 days ago by
Sam
★ 3.4k • written 5 days ago by
simone.castellana
▴ 10
0
votes
0
replies
45
views
Partitioning heritability
Heritability
Partition
GWAS
6 days ago by
aelhossiny
• 0
0
votes
2
replies
190
views
GAPIT error : invalid '(to - from)/by'
GWAS
R
programming
14 days ago by
Inquisitive8995
▴ 210
0
votes
0
replies
87
views
Using SAIGE for GWAS without including covariates
SNP
GWAS
vcf
plink
SAIGE
20 days ago by
mfshiller
▴ 10
0
votes
20
replies
415
views
Mixed Linear Model and GWAS study
GWAS
SNPs
Mixed Liner Model
TASSEL
20 days ago by
Manoj
▴ 100
0
votes
0
replies
72
views
How to add legend in Adegenet at R
GWAS
SNPs
R
20 days ago by
Manoj
▴ 100
0
votes
0
replies
85
views
How to perform custom annotation using garfield_annotate_uk10k.sh script in GARFIELD tool?
awk
R
GWAS
bash
20 days ago by
bk11
▴ 40
3
votes
3
replies
329
views
GWAS Summary statistic
gwas
20 days ago by
Kevin
• 0
0
votes
0
replies
153
views
Is it possible to impute missing phenotypes (case/control) in Plink .fam files in a GWAS study?
illumina
plink
GWAS
IDAT
26 days ago by
doughan.albert
• 0
0
votes
0
replies
99
views
GWAS q-q plot showing lots of "1's" and a flat line with logistic regression
gwas
qqplot
plink
4 weeks ago by
Vanish007
▴ 10
0
votes
0
replies
91
views
Q-Q plot for p-value from HWE exact test
Q-Q plot
Hardy-Weinberg
p-value
GWAS
QC
4 weeks ago by
panacotaforcota
• 0
3
votes
4
replies
155
views
Unused command line option: --make-just-fam
plink
GWAS
linux
updated 4 weeks ago by
davidenoma
▴ 50 • written 4 weeks ago by
suraj.adewale1
• 0
0
votes
0
replies
71
views
GWAS LocusZoom Plot from .CSV
gwas
plotting
4 weeks ago by
abyousaf
• 0
0
votes
0
replies
92
views
Impute2 empty output for imputed SNPs
impute2
SNP
sequencing
genome
GWAS
5 weeks ago by
kittys
• 0
1
vote
2
replies
124
views
[PLINK] Error: Duplicate ID when running an --update-ids
Plink
GWAS
SNP
software error
Tool
updated 5 weeks ago by
ashishjayamohan
• 0 • written 5 weeks ago by
njofrica
▴ 10
0
votes
0
replies
149
views
Good practice for merging different sets of Plink data files
Plink
GWAS
5 weeks ago by
guessit
• 0
1
vote
10
replies
185
views
ERROR::: vcf to PLINK
PLINK
GWAS
VCFs
updated 5 weeks ago by
Sam
★ 3.4k • written 5 weeks ago by
Manoj
▴ 100
0
votes
1
reply
118
views
Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
HWE
GWAS
updated 5 weeks ago by
curious
▴ 500 • written 5 weeks ago by
USA_225478
• 0
0
votes
3
replies
170
views
ERROR with METAL
gwas
metal
meta-analysis
error
updated 6 weeks ago by
bjyxszd
• 0 • written 11 weeks ago by
d.s.zimmerman
• 0
0
votes
0
replies
283
views
Tool:
I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
GWAS
visualization
genome
Python
Manhattan Plot
Tool
6 weeks ago by
huangshujia9
• 0
1
vote
4
replies
152
views
Forum:
Very high ratio of cases to controls - how to increase statistical power?
gwas
SNP
Forum
6 weeks ago by
mfshiller
▴ 10
0
votes
0
replies
410
views
Job:
Post-doc position in multi-omics of Alzheimer's disease at Columbia University in New York City
sequencing
post-doc
multiomics
R
GWAS
Job
6 weeks ago by
lhd
• 0
3
votes
5
replies
640
views
Post-imputation QC GWAS analysis
GWAS
Rstudio
Imputation
TopMed
updated 7 weeks ago by
Biostar
20 • written 7 months ago by
AR
• 0
0
votes
1
reply
367
views
How to interpret logistic interaction results from plink2 output?
SNP
plink
GWAS
interaction
logistic
updated 7 weeks ago by
Kevin Blighe
72k • written 12 months ago by
aj
• 0
0
votes
0
replies
92
views
whole genome sequence -meta analysis
next-gen
gwas
gcta
genome
7 weeks ago by
Neu
▴ 10
0
votes
2
replies
164
views
How to do pca plot from .eigenvec files from Plink in R
R
GWAs
Plink
7 weeks ago by
anithanagaraj93
• 0
0
votes
1
reply
123
views
Making PLINK compatible files from VCF file without phenotype information
plink
gwas
vcf
8 weeks ago by
mfshiller
▴ 10
2
votes
2
replies
163
views
Error attaching phenotype in PLINK (fewer tokens than expected)
GWAS
PLINK
8 weeks ago by
absoldini
▴ 10
4
votes
6
replies
782
views
GWAS missing p-values
software error
snp
genome
GWAS
logistic regression
updated 8 weeks ago by
hkj7
• 0 • written 2.2 years ago by
emmacomp
▴ 10
0
votes
0
replies
169
views
How to investigate population structure
GWAS
VCFs
genome
Assembly
8 weeks ago by
Manoj
▴ 100
0
votes
3
replies
174
views
How to merge vcf files
VCFs
GWAS
genome
updated 8 weeks ago by
4galaxy77
▴ 390 • written 8 weeks ago by
Manoj
▴ 100
0
votes
1
reply
133
views
Mapping DNA position to Protein Position in E. Coli
genomics
bioinformatics
gwas
sequencing
updated 8 weeks ago by
Emily_Ensembl
22k • written 8 weeks ago by
Negin
▴ 10
1
vote
6
replies
228
views
Using GNU parallel to speed up merging VCFs with bcftools
vcf
parallel
gwas
bcftools
bash
8 weeks ago by
mfshiller
▴ 10
1
vote
2
replies
188
views
Duplicate SNP IDs in TOPMed Imputation output for gwas data
topmed
gwas
imputation
SNP
snp
updated 9 weeks ago by
Kevin Blighe
72k • written 9 weeks ago by
yy237
▴ 30
1
vote
2
replies
125
views
Going from GWAS SNPs to disproportionately affected genes
gwas
SNP
gene
9 weeks ago by
mfshiller
▴ 10
0
votes
3
replies
1.2k
views
Why there is no beta of SE output in some meta GWAS results?
gwas
meta
beta
SE
updated 10 weeks ago by
DM
▴ 20 • written 2.0 years ago by
lilingjoyo
▴ 40
0
votes
0
replies
163
views
Using PLINK for generating PC/MDS for GWAS
gwas
PLINK
PCA
MDS
prune
10 weeks ago by
arctic
▴ 20
0
votes
1
reply
130
views
Combine BedTools Closest and Window Command
SNP
genome
sequencing
bedtools
GWAS
11 weeks ago by
Dotty
• 0
0
votes
2
replies
305
views
compare two GWAS results
GWAS
SNP
updated 11 weeks ago by
DM
▴ 20 • written 4 months ago by
sihambarkus
• 0
1
vote
2
replies
163
views
Bacterial GWAS analysis
Bacteria
Gwas
vcflib
11 weeks ago by
Manasa
• 0
4
votes
3
replies
2.8k
views
Mirror Manhattan Plot
qqman
manhattan
GWAS
plot
R
updated 12 weeks ago by
DM
▴ 20 • written 4.2 years ago by
jennysjaarda
▴ 10
3
votes
0
replies
715
views
Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?
BOLT-LMM
SAIGE
GWAS
replication of results
updated 12 weeks ago by
GenoMax
99k • written 12 weeks ago by
futurolog
▴ 30
1
vote
1
reply
283
views
Why does GWAS Catalog mix OR and beta in the same column?
GWAS
gwas_catalog
OR
updated 12 weeks ago by
zhoufeng2ye
• 0 • written 9 months ago by
Juan Manuel Berros
▴ 90
0
votes
5
replies
144
views
How to get independent loci from gwas variants
gwas
R
snp
sequencing
python
3 months ago by
morse.endeavour86
• 0
1
vote
3
replies
164
views
Math behind association with PLINK
plink
association
gwas
updated 3 months ago by
rpolicastro
5.1k • written 3 months ago by
Will
• 0
0
votes
4
replies
394
views
Convert ped/bed into CSV/text file
GWAS
Machine Learning
plink
updated 3 months ago by
Biostar
20 • written 5 months ago by
Dhara Awasthi
▴ 30
0
votes
0
replies
158
views
Deviance in allele frequencies between arrays and WGS
GWAS
PRS
WGS
array
3 months ago by
German.M.Demidov
★ 2.0k
0
votes
1
reply
197
views
Plotting the results (p-values) from various conditional GWAS
GWAS
PLOT
updated 3 months ago by
devarora
▴ 430 • written 3 months ago by
sam.far.7
• 0
861 results • Page
1 of 18
Recent Votes
Comment: why my volcano plot looks strange?
C: how to choose hub genes in wgcna
C: Variant Calls: Freebayes vs GATK
C: Variant Calls: Freebayes vs GATK
A: FreeBayes vs GATK's HaplotypeCaller
Comment: why my volcano plot looks strange?
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Recent Locations •
All
University Park, USA,
just now
Lithuania,
1 minute ago
United Kingdom,
1 minute ago
Norway,
2 minutes ago
Oviedo,
3 minutes ago
Pennsylvania,
3 minutes ago
Brazil,
3 minutes ago
Recent Awards •
All
Scholar
to
JC
12k
Commentator
to
5heikki
9.7k
Scholar
to
bernatgel
★ 2.9k
Scholar
to
Joe
19k
Scholar
to
Devon Ryan
98k
Scholar
to
igor
12k
Appreciated
to
Jean-Karim Heriche
24k
Recent Replies
Comment: FreeBayes vs GATK's HaplotypeCaller
by
cicindel
▴ 70
I think file size, based on the following sentence.
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
I don't see `GENE` being assigned values, so I'm guessing there is yet another loop wrapping the code above. Write the value of `GENE` to s…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴ 70
Interesting, I did not think about it like that. Tablet has several colour schemes in the 2nd tab (I think) to visualize different features…
Answer: Trimmomatic-0.36 not finding adapter directory
by
Istvan Albert
87k
Download the adapters and use them by passing the actual path, existing paths to the adapter file. See the adapters here https://git…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
Istvan Albert
87k
in all fairness, Tablet did not exist when this thread was started. It is quite impressive that Tablet is still operational though, I gave …
Comment: Trimmomatic-0.36 not finding adapter directory
by
GenoMax
99k
Order of `fastq` file names is important for `trimmomatic`. Make sure that is correct.<br> Does `ls -lh /usr/local/bin/Trimmomatic-0.36/` …
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴ 70
No love for [Tablet][1]? I'm quite surprised to not see it mentioned here. Of course, IGV is the classic, and Tablet is a bit simpler than …
Comment: How to download raw sequence data from GEO/SRA
by
cicindel
▴ 70
I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ?
by
cpad0112
15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
good luck!
Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
by
geneticatt
▴ 120
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Traffic: 2424 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6