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6,493 results • Page
1 of 130
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Filtering for tag:
SNP
•
reset
2
votes
2
replies
533
views
Recombination maps for cattle
SNP
IMPUTE2
genome
Assembly
updated 2 hours ago by
Azwan
• 0 • written 18 months ago by
mdyogolos
▴ 10
0
votes
0
replies
22
views
JoinMap4 makes a new map every time
joinmap
linkage_mapping
genetic_map
SNP
7 hours ago by
Beetle Editor
• 0
0
votes
1
reply
48
views
Detection of bacterial SNP using regular PCR primers
detection
PCR
SNP
updated 11 hours ago by
David Parry
▴ 60 • written 12 hours ago by
Audrey
▴ 50
0
votes
2
replies
469
views
freebayes for snp call in pooled samples: how do I set the parameters?
SNP
freebayes
pooled
ploidy
updated 1 day ago by
ross_whetten
▴ 10 • written 12 months ago by
cristiana.ij.marques
• 0
2
votes
6
replies
285
views
Generate a file with SNPs given a WGS dataset
annotation
snp
ngs
22 hours ago by
iibrams07
• 0
1
vote
3
replies
346
views
Keep values from VCF file into Ensembl VEP annotation
SNP
updated 1 day ago by
dare_devil
★ 1.4k • written 3 months ago by
brunobsouzaa
▴ 520
0
votes
0
replies
1.2k
views
In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
snp
kissplice
rna-seq
stack
KisSplice
3 days ago by
ec-ho-ra-mos
• 0
1
vote
1
reply
86
views
PCA plot making
VCF
PCA
vcftools
SNP
updated 3 days ago by
prasundutta87
▴ 470 • written 3 days ago by
yb87625
• 0
0
votes
0
replies
82
views
SNP Mapping/Characterisation and Patches
GRCh38
prioritisation
patches
SNP
3 days ago by
KBMP
• 0
0
votes
0
replies
39
views
Active regions determination in HaplotypeCaller
SNP
GATK
VCF
HaplotypeCaller
BAM
5 days ago by
Nawar
• 0
2
votes
1
reply
91
views
Plot SNPs on transcripts
transcripts
SNP
gene
plot
updated 5 days ago by
colindaven
★ 2.7k • written 5 days ago by
g.papprank
▴ 10
0
votes
1
reply
65
views
Multiple Transctipr ID (NM ) from MyVariantInfo
snp
transcript
dna-seq
updated 5 days ago by
prasundutta87
▴ 470 • written 5 days ago by
hkarakurt
▴ 110
0
votes
0
replies
52
views
bootstrapping help
genome
bootstrap
vcf
bootstrapping
SNP
6 days ago by
truebeliever24
▴ 20
0
votes
0
replies
411
views
How to combine multiple snp array datasets on different versions of same array design (GSA) ?
array
different
GSA
snp
version
6 days ago by
lax
• 0
0
votes
1
reply
142
views
SNP's datasets and pedigreees
SNP
data
inference
haplotype
pedigrees
base
updated 9 days ago by
Sam
★ 3.4k • written 9 days ago by
S. Roa
• 0
8
votes
9
replies
1.7k
views
Where can I lookup old merged rsIDs?
SNP
updated 8 days ago by
Vince Carey
▴ 80 • written 4.1 years ago by
Mike Dacre
▴ 130
0
votes
1
reply
98
views
How are SNP distance matrices made?
matrix
SNP
distance
CFSAN
pipeline
updated 12 days ago by
Istvan Albert
87k • written 13 days ago by
braun_tube
▴ 10
1
vote
1
reply
143
views
Calculate allele frequencies per population with SNPRelate
SNPRelate
allelefrequencies
plink
SNP
R
updated 14 days ago by
cicindel
▴ 60 • written 18 days ago by
irieljoerin
▴ 40
22
votes
19
replies
3.2k
views
7 follow
FastQTL - GNU Scientific Library (GSL) Domain Error
eQTL
GSL
RNA-Seq
SNP
FastQTL
updated 15 days ago by
haroonnaim
• 0 • written 4.1 years ago by
maegsul
▴ 170
3
votes
4
replies
244
views
Excluding variants with a "LowQual" filter in bcftools consensus
snp
bcftools
covid-19
ngs
16 days ago by
cg1440
▴ 20
5
votes
1
reply
132
views
How to evaluate phylogenetic congruence between two phylogenetic tree?
snp
python
perl
genomics
phylogeny
updated 17 days ago by
Mensur Dlakic
★ 10k • written 17 days ago by
Kumar
▴ 50
3
votes
7
replies
420
views
How to calculate frequencies of SNPs with respect to a particular allele by plink?
frequency
snp
plink
17 days ago by
jamespower
▴ 50
1
vote
8
replies
345
views
How to split text into columns using R
snp
updated 13 days ago by
cpad0112
15k • written 17 days ago by
shubhamkumbhar420
• 0
0
votes
0
replies
91
views
Combine populations.samples.fa alleles using STACKS
rad
snp
haplotype
vcf
updated 18 days ago by
Kevin Blighe
72k • written 18 days ago by
mr.two
• 0
1
vote
4
replies
2.0k
views
Annotate Ref/Alt for a list of rsIDs?
dbSNP
snp
updated 18 days ago by
GenoMax
99k • written 3.6 years ago by
blazer9131
▴ 20
5
votes
4
replies
2.0k
views
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
conversion
SNP
Tool
updated 18 days ago by
CoolEvilgenius
• 0 • written 20 months ago by
Macspider
★ 3.4k
0
votes
0
replies
73
views
How to know the number of SNP after running the population module using stacks
population
snp
updated 19 days ago by
ATpoint
47k • written 19 days ago by
virtualinterlect
• 0
1
vote
6
replies
320
views
how to extract content from dbSNP database using set of "rsid's".
dbSNP
rsid
dataretrieval
database
snp
19 days ago by
deepak.deucy
▴ 10
0
votes
0
replies
72
views
KING relationship inference, problem with sheep population
king
kinship
snp
sheep
genome
19 days ago by
maxysha95
• 0
0
votes
0
replies
84
views
Using SAIGE for GWAS without including covariates
SNP
GWAS
vcf
plink
SAIGE
19 days ago by
mfshiller
▴ 10
1
vote
0
replies
68
views
xpEHH
genomics
test
snp
20 days ago by
dominik.lagler
▴ 10
0
votes
0
replies
75
views
How to do clustering of SNPs according to linkage disequilibrium (r2) values?
nex-gen
R
rna-seq
snp
genome
21 days ago by
anikcropscience
▴ 40
0
votes
2
replies
145
views
Why PLINK is producing different LD result with the same dataset?
SNP
sequence
genome
R
software error
updated 22 days ago by
Sam
★ 3.4k • written 23 days ago by
anikcropscience
▴ 40
0
votes
0
replies
117
views
Arlequin problem (different loci number among different genotypes)
SNP
23 days ago by
wangh920
• 0
7
votes
9
replies
199
views
6 follow
Bioinformatics research work
genome
snp
assembly
updated 23 days ago by
Michael Dondrup
48k • written 23 days ago by
sa2020ad1
• 0
0
votes
6
replies
185
views
How to keep only Biallelic SNP in vcf
snp
updated 23 days ago by
Pierre Lindenbaum
135k • written 23 days ago by
wangh920
• 0
2
votes
0
replies
1.4k
views
Confusion over SNP strand importance re genotyping (G>C)
taqman
genotyping
strand
dna
SNP
updated 24 days ago by
Biostar
20 • written 4.6 years ago by
oooner2014
▴ 20
0
votes
1
reply
100
views
How to convert plink data from 38th assembly to 37
assembly
SNP
plink
liftOver
genome
24 days ago by
eyb
▴ 210
1
vote
2
replies
2.0k
views
How to do Tajima's D analysis?
snp
genome
updated 24 days ago by
Biostar
20 • written 3.0 years ago by
amitgourav.ghosh12
▴ 70
0
votes
1
reply
380
views
SNPs density ( count/ per Kb) calculation from VCF file
SNP
SNPs density
Count/Kb
updated 25 days ago by
mgalland1983
▴ 10 • written 5 months ago by
BioRyder
▴ 180
2
votes
3
replies
129
views
Effect of removing secondary/supplementary alignments from BAM file?
ngs
covid-19
SNP
25 days ago by
cg1440
▴ 20
3
votes
5
replies
112
views
PLINK:Error: Variant '.' is not biallelic. To obtain a full list of merge failures
SNP
Assembly
genome
next-gen
25 days ago by
williamsbrian5064
▴ 380
1
vote
2
replies
86
views
merge paired-end sequencing
SNP
merge
gatk
25 days ago by
gubrins
▴ 70
0
votes
0
replies
82
views
Mapping after WGS show a parabel form
WGS
mapping
SNP
CNV
25 days ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
114
views
Identifiying SNP frequencies for very specific subpopulations on dbSNP
SNP
26 days ago by
Michael
▴ 210
0
votes
3
replies
101
views
change missing genotype in bcf file from 0/0 to ./. to run plink
bcftools
plink
SNP
genotype
bcf
26 days ago by
rah
▴ 20
1
vote
2
replies
96
views
In-silico downsizing to estimate the DNA input
sequencing
snp
next-gen
updated 26 days ago by
5heikki
9.6k • written 26 days ago by
APJ
▴ 30
0
votes
2
replies
112
views
How to perform Linkage Disequilibrium analysis for significantly associated K-mers?
next-gen
genome
snp
assembly
updated 26 days ago by
biostarter
• 0 • written 28 days ago by
anikcropscience
▴ 40
0
votes
2
replies
251
views
Repeated measures in GWAS and polygenic risk scores analyses
SNP
updated 26 days ago by
yanlea
• 0 • written 12 months ago by
kl
▴ 10
0
votes
1
reply
204
views
conversion of a genlight object into a genpop object
snp
R
updated 26 days ago by
nandhakishorekj97
• 0 • written 7 months ago by
satish.vety
• 0
6,493 results • Page
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Recent Votes
Comment: Finding how many times a nucleotide appear in the same position
Plotting Differential Induced Genes across timepoints in DESEQ2
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Comment: Meaning of BWA-MEM MAPQ values
A: Detecting highly variable genes within replicates
A: Detecting highly variable genes within replicates
Answer: Pooling normal data in Mutect2
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Answer: Plotting Differential Induced Genes across timepoints in DESEQ2
by
raisamathenge
▴ 10
I have had problems with using an interaction term between stimulus and timepoint that was not able to run as well. How can I fix that? I w…
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by
kristina.mahan
▴ 130
The sequencing coverage is >200x
Answer: Plotting Differential Induced Genes across timepoints in DESEQ2
by
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9.7k
I don't think you need the "1" in the design; I've never seen that in any DESeq tutorial. What your design will do is compare the betas …
Comment: Plotting Differential Induced Genes across timepoints in DESEQ2
by
raisamathenge
▴ 10
![Here is my ColData][1] [1]: /media/images/f2f1b815-3669-4525-9636-c6dc193e
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Hi I managed to **add DE tags to the plotMD** using the code I published on Kaggle: [Kaggle DE analysis][1] Here is an example of the co…
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Calculating statistics, be it Z- or whatever score, is still based on some kind of data, and I wonder whether it is motifs or actual bindin…
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Can you show your `colData` to understand how the groups are set up?
Comment: Finding how many times a nucleotide appear in the same position
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Pierre Lindenbaum
135k
cross posted: https://stackoverflow.com/questions/67060118/
Comment: What to put in my Github
by
GenoMax
99k
Since this is an open-ended question I am changing it to `Forum`. > I am not allowed to release my scripts or data Unless you are doing s…
Answer: What to put in my Github
by
jared.andrews07
9.2k
Yes, I think analyzing publicly available data is perfectly fine. Trying to reproduce their findings (or find something they perhaps missed…
Comment: Recombination maps for cattle
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Azwan
• 0
Hi did you found it?
Comment: How can I create an Illumina report in Linux using IDAT files?
by
freeseek
▴ 120
You can look at the full content of a GTC file with the following command: ``` bcftools +gtc2vcf -v <file.gtc> ```
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Pierre Lindenbaum
135k
get the complement BED use `bedtools complement` and the scan the bam using samtools view -L complement.bed
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