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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 • 0 • written 18 months ago by ▴ 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 ▴ 60 • written 12 hours ago by ▴ 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 ▴ 10 • written 12 months ago by • 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 ★ 1.4k • written 3 months ago by ▴ 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 ▴ 470 • written 3 days ago by • 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 ★ 2.7k • written 5 days ago by ▴ 10
0
votes
1
reply
65
views
Multiple Transctipr ID (NM ) from MyVariantInfo
snp transcript dna-seq
updated 5 days ago by ▴ 470 • written 5 days ago by ▴ 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 ★ 3.4k • written 9 days ago by • 0
8
votes
9
replies
1.7k
views
Where can I lookup old merged rsIDs?
SNP
updated 8 days ago by ▴ 80 • written 4.1 years ago by ▴ 130
0
votes
1
reply
98
views
How are SNP distance matrices made?
matrix SNP distance CFSAN pipeline
updated 12 days ago by 87k • written 13 days ago by ▴ 10
1
vote
1
reply
143
views
Calculate allele frequencies per population with SNPRelate
SNPRelate allelefrequencies plink SNP R
updated 14 days ago by ▴ 60 • written 18 days ago by ▴ 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 • 0 • written 4.1 years ago by ▴ 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 ★ 10k • written 17 days ago by ▴ 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 15k • written 17 days ago by • 0
0
votes
0
replies
91
views
Combine populations.samples.fa alleles using STACKS
rad snp haplotype vcf
updated 18 days ago by 72k • written 18 days ago by • 0
1
vote
4
replies
2.0k
views
Annotate Ref/Alt for a list of rsIDs?
dbSNP snp
updated 18 days ago by 99k • written 3.6 years ago by ▴ 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 • 0 • written 20 months ago by ★ 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 47k • written 19 days ago by • 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 ★ 3.4k • written 23 days ago by ▴ 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 48k • written 23 days ago by • 0
0
votes
6
replies
185
views
How to keep only Biallelic SNP in vcf
snp
updated 23 days ago by 135k • written 23 days ago by • 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 20 • written 4.6 years ago by ▴ 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 20 • written 3.0 years ago by ▴ 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 ▴ 10 • written 5 months ago by ▴ 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 9.6k • written 26 days ago by ▴ 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 • 0 • written 28 days ago by ▴ 40
0
votes
2
replies
251
views
Repeated measures in GWAS and polygenic risk scores analyses
SNP
updated 26 days ago by • 0 • written 12 months ago by ▴ 10
0
votes
1
reply
204
views
conversion of a genlight object into a genpop object
snp R
updated 26 days ago by • 0 • written 7 months ago by • 0
6,493 results • Page 1 of 130
Recent Votes
Comment: Finding how many times a nucleotide appear in the same position
Plotting Differential Induced Genes across timepoints in DESEQ2
Answer: What to put in my Github
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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Recent Replies
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…
Comment: What Coverage allele-fraction threshold to use? by kristina.mahan ▴ 130
The sequencing coverage is >200x
Answer: Plotting Differential Induced Genes across timepoints in DESEQ2 by swbarnes2 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
Answer: How to highlight DE genes in plotMD ? by raulgcova97 • 0
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…
Comment: transcription factor activation order by ATpoint 47k
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…
Comment: What to put in my Github by ATpoint 47k
Seconding that. I strongly encourage everyone to wrap commonly used code and functions as simple packages and put them on Github. This allo…
Comment: Quantify inactivated virus particles by ATpoint 47k
This post is off topic as not bioinformatics-related. I suggest you ask this in a suitable subreddit or at ResearchGate (or similar platfor…
Comment: Plotting Differential Induced Genes across timepoints in DESEQ2 by ATpoint 47k
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 by 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 by 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> ```
Answer: Samtools view filter by reference sequence by 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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