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Showing :
questions
0
votes
2
replies
488
views
Low coverage whole genome sequencing reveal excess heterozygosity for multiple SNPs. How to filter?
lcWGS
WGS
heterozygosity
5 months ago by
beausoleilmo
▴ 580
0
votes
0
replies
301
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 11 months ago by
Ram
43k • written 11 months ago by
beausoleilmo
▴ 580
2
votes
0
replies
614
views
How to convert a Beagle file 3.3 to VCF with beagle2vcf.jar?
conversion
vcf
beagle
17 months ago by
beausoleilmo
▴ 580
0
votes
2
replies
577
views
Left or right join between 2 BAM files (remove reads the should be filtered out for sex chromosomes)
sex
chromosomes
BAM
filtering
17 months ago by
beausoleilmo
▴ 580
2
votes
2
replies
849
views
How to rename chromosome_position column in a Beagle file and match it with the index fai?
chromosome
index
fai
regex
beagle
updated 19 months ago by
Jukka Matilainen
▴ 80 • written 19 months ago by
beausoleilmo
▴ 580
2
votes
5
replies
2.0k
views
Is there a way to calculate breadth of coverage from a VCF?
VCF
Coverage
Beagle
19 months ago by
beausoleilmo
▴ 580
2
votes
2
replies
2.2k
views
Error running sam-dump
sam
NCBI
BAM
samtools
updated 3.7 years ago by
Biostar
20 • written 7.5 years ago by
beausoleilmo
▴ 580
2
votes
8
replies
1.7k
views
Detect sex chromosomes from WGS on a bird species (with reference genome)
WGS
chromosomes
updated 2.8 years ago by
clinnaeus
▴ 30 • written 4.2 years ago by
beausoleilmo
▴ 580
6
votes
5
replies
4.6k
views
Error while creating .geno file with LEA
LEA
geno
VCF
3.0 years ago by
beausoleilmo
▴ 580
1
vote
0
replies
1.6k
views
Building a reference database for metabarcoding and obitools
embl
metabarcoding
reference database
plants
diet
4.2 years ago by
beausoleilmo
▴ 580
8
votes
6
replies
7.2k
views
6 follow
How to parallelize bcftools mpileup with GNU parallel?
bcftools
mpileup
parallel
updated 2.5 years ago by
Sarah
▴ 60 • written 4.3 years ago by
beausoleilmo
▴ 580
16
votes
3
replies
11k
views
What is the difference between mpileup samtools and bcftools?
bcftools
samtools
mpileup
variant calling
SNP
updated 4.3 years ago by
jkbonfield
★ 1.2k • written 4.3 years ago by
beausoleilmo
▴ 580
7
votes
6
replies
4.9k
views
Running BWA mem in a for loop
BWA
alignment
WGS
updated 4.3 years ago by
Gio12
▴ 220 • written 4.3 years ago by
beausoleilmo
▴ 580
2
votes
2
replies
1.2k
views
ecoPCR won't install on Mac (Mojave 10.14.5)
ecoPCR
metabarcoding
4.6 years ago by
beausoleilmo
▴ 580
1
vote
1
reply
1.1k
views
Chromosome naming convention: Why are there chromosomes named "1" and "1A"?
Chromosome
Zebra Finch
4.6 years ago by
beausoleilmo
▴ 580
6
votes
6
replies
1.8k
views
Is it a problem that the reference genome is not at the chromosome level?
Chromosome
reference genome
scaffolds
updated 4.7 years ago by
Brice Sarver
★ 3.8k • written 4.7 years ago by
beausoleilmo
▴ 580
0
votes
2
replies
1.9k
views
How to process degenerate base region (DBRs) in a ddRAD sequencing protocol (remove PCR duplicates)?
ddRAD
next-gen
Stacks
DBR
updated 11 months ago by
Ram
43k • written 6.6 years ago by
beausoleilmo
▴ 580
0
votes
3
replies
1.3k
views
What is the definition of "multiply aligned" sequences compared to multiple aligned sequence
sequence
DNA
alignment
5.9 years ago by
beausoleilmo
▴ 580
5
votes
5
replies
1.6k
views
Is whole genome pool-sequencing a reduced representation sequencing technique?
whole genome
DNA sequencing
updated 6.0 years ago by
h.mon
35k • written 6.0 years ago by
beausoleilmo
▴ 580
10
votes
4
replies
4.6k
views
Difference between Allele frequency spectrum and Joint allele frequency spectrum
allele
population structure
updated 11 months ago by
jena
▴ 290 • written 6.0 years ago by
beausoleilmo
▴ 580
0
votes
0
replies
1.2k
views
Is there a way to construct a pedigree using RADseq data?
RAD sequencing
pedigree
6.1 years ago by
beausoleilmo
▴ 580
3
votes
3
replies
14k
views
What is population branch statistic (PBS)?
population structure
FST
Natural Selection
updated 6.2 years ago by
GabrielMontenegro
▴ 670 • written 6.2 years ago by
beausoleilmo
▴ 580
4
votes
1
reply
7.7k
views
How is it possible to create a .fam file with PLINK with phenotypic data (for GEMMA)?
plink
fam
vcftools
Gemma
updated 6.5 years ago by
Kevin Blighe
87k • written 7.4 years ago by
beausoleilmo
▴ 580
7
votes
2
replies
1.8k
views
Why is there a star in some primer sequences (library preparation)
sequencing
library
DNA
updated 6.7 years ago by
WouterDeCoster
47k • written 6.7 years ago by
beausoleilmo
▴ 580
3
votes
3
replies
4.6k
views
What is the difference between a small-insert library, large-insert library and the reads themselves?
sequencing
updated 6.8 years ago by
Brian Bushnell
20k • written 6.8 years ago by
beausoleilmo
▴ 580
0
votes
2
replies
1.2k
views
What are modules and reactions in NGS?
NGS
sequencing
6.9 years ago by
beausoleilmo
▴ 580
3
votes
3
replies
2.4k
views
Is RADseq the same thing as Shotgun sequencing?
RADseq
Shotgun sequencing
updated 7.0 years ago by
h.mon
35k • written 7.0 years ago by
beausoleilmo
▴ 580
13
votes
17
replies
7.6k
views
Why is FastQC not working after using Trim galore?
fastq
FASTQC
Fastqc
updated 7.1 years ago by
h.mon
35k • written 7.8 years ago by
beausoleilmo
▴ 580
4
votes
4
replies
4.5k
views
VCFtools --minDP flags not working
vcftools
Read Depth
7.2 years ago by
beausoleilmo
▴ 580
6
votes
11
replies
6.1k
views
Converting PLINK to EIGENSTRAT error using convertf (no valid snps)
EIGENSTRAT
PLINK
SNP
PCA
updated 7.2 years ago by
LauferVA
4.2k • written 7.2 years ago by
beausoleilmo
▴ 580
3
votes
1
reply
3.0k
views
Is there a way to tell PLINK and VCFtools to sort the samples in a particular order?
PLINK
VCFtools
sort
ped
bed
updated 7.3 years ago by
chrchang523
10k • written 7.3 years ago by
beausoleilmo
▴ 580
1
vote
0
replies
3.3k
views
What does the -A "Matching score" and -B "Mismatch penalty" flags doing in BWA mem?
BWA
Matching score
penalty
GWAS
7.3 years ago by
beausoleilmo
▴ 580
0
votes
0
replies
1.1k
views
filtering tips for GWAS studies (admixture mapping)
vcftools
filtering
GWAS
VCF
7.3 years ago by
beausoleilmo
▴ 580
3
votes
1
reply
9.0k
views
How to order Admixture (ancestry) plot in R
ADMIXTURE
R
q plot
updated 7.3 years ago by
Joseph Hughes
★ 3.0k • written 7.3 years ago by
beausoleilmo
▴ 580
12
votes
9
replies
2.9k
views
Why is it absolutely necessary to filter a VCF?
VCF
bcftools
vcftools
samtools
filtering
updated 7.3 years ago by
mforde84
★ 1.4k • written 7.3 years ago by
beausoleilmo
▴ 580
0
votes
0
replies
2.4k
views
ADMIXTURE, size of .bed file not matching number of individuals in analysis
ADMIXTURE
7.3 years ago by
beausoleilmo
▴ 580
6
votes
1
reply
3.7k
views
What does Number=0/Number=1 mean in a VCF?
VCF
DNA
GWAS
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
beausoleilmo
▴ 580
3
votes
4
replies
2.6k
views
How common are Deletions and Indels?
VCFtools
RTG
RADseq
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
beausoleilmo
▴ 580
0
votes
0
replies
2.4k
views
VCFtools filter missing genotypes conditional on a factor (population, species, etc.)
VCFtools
Filter
NGS
RAD
7.3 years ago by
beausoleilmo
▴ 580
1
vote
2
replies
1.7k
views
Can Scaffolds overlap?
Scaffolds
contigs
RADseq
7.3 years ago by
beausoleilmo
▴ 580
0
votes
0
replies
1.7k
views
Is GEMMA able to run a bayesian sparse linear mixed model with the sex column?
plink
GWAS
GEMMA
fam
updated 13 months ago by
Ram
43k • written 7.3 years ago by
beausoleilmo
▴ 580
1
vote
5
replies
2.8k
views
Association mapping with plink: what type of phenotypic data?
PLINK
association mapping
GWAS
SNP
VCF
updated 7.3 years ago by
Fabio Marroni
★ 3.0k • written 7.4 years ago by
beausoleilmo
▴ 580
3
votes
2
replies
2.7k
views
How should the data be formatted to run an association mapping in PLINK?
PLINK
association mapping
VCF
Phenotype
GWAS
updated 7.4 years ago by
Sarthok
▴ 70 • written 7.4 years ago by
beausoleilmo
▴ 580
1
vote
4
replies
2.7k
views
How to map BAM file to reference genome "[fai_fetch_seq] The sequence not found"
Fasta
reference genome
BAM
updated 7.4 years ago by
Biostar
20 • written 7.5 years ago by
beausoleilmo
▴ 580
0
votes
5
replies
2.7k
views
VCFtools alternative to --minDP flags not working?
VCF
Read Depth
updated 7.4 years ago by
igor
13k • written 7.4 years ago by
beausoleilmo
▴ 580
2
votes
4
replies
3.9k
views
Is it possible to count the number of loci in a VCF file?
VCF
SNP
Loci
updated 7.4 years ago by
Pierre Lindenbaum
161k • written 7.4 years ago by
beausoleilmo
▴ 580
16
votes
12
replies
9.7k
views
Replace names in FASTA file with a known character string from a text file
FASTA
updated 7.5 years ago by
shenwei356
8.5k • written 7.5 years ago by
beausoleilmo
▴ 580
0
votes
9
replies
2.9k
views
File size on NCBI
NCBI
BAM
SAM
7.5 years ago by
beausoleilmo
▴ 580
10
votes
19
replies
3.2k
views
Installing Stacks on a cluster problem with Make install
software error
updated 7.7 years ago by
John Marshall
3.0k • written 7.7 years ago by
beausoleilmo
▴ 580
49 results • Page
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