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Showing :
questions
3
votes
3
replies
1.1k
views
ancestral allele SNP mouse biomart
biomart
ensembl
mouse
snp
updated 2.6 years ago by
Emily
23k • written 2.6 years ago by
serpalma.v
▴ 80
0
votes
0
replies
614
views
Evaluating RMSMappingQuality profile to set threshold
SNP
snp
gatk
variant calling
filtering
updated 3.9 years ago by
Nicolas Rosewick
11k • written 3.9 years ago by
serpalma.v
▴ 80
8
votes
8
replies
3.2k
views
Only females but still few reads map to Y chromosome
bwa
WGS
alignment
updated 3.9 years ago by
Biostar
20 • written 5.5 years ago by
serpalma.v
▴ 80
1
vote
2
replies
974
views
Insert size 350bp vs 400bp, any major downstream difference?
SNP
alignment
sequencing
4.0 years ago by
serpalma.v
▴ 80
0
votes
0
replies
757
views
how can I extract intervals from bed file spanning a max larger interval in a windowed mode without disrupting intervals?
sequencing
bed
bedtools
bedops
4.1 years ago by
serpalma.v
▴ 80
1
vote
3
replies
1.2k
views
How to extract intervals for regions that are masked?
SNP
sequencing
assembly
4.1 years ago by
serpalma.v
▴ 80
1
vote
7
replies
1.5k
views
Are there any issues with using sample reads coming from different technologies and having different depths to do joint variant calling (gatk)?
gatk
SNP
variant calling
hiseq
novaseq
updated 4.2 years ago by
bari.ballew
▴ 460 • written 4.2 years ago by
serpalma.v
▴ 80
2
votes
1
reply
2.5k
views
How to replicate vcftool's sliding window SNP density?
SNP
sequencing
vcftools
updated 4.6 years ago by
Vitis
★ 2.5k • written 4.6 years ago by
serpalma.v
▴ 80
0
votes
2
replies
1.9k
views
How does plink calculates linkage disequilibrium (r2) in unphased data?
plink
SNP
sequencing
updated 4.7 years ago by
chrchang523
10k • written 4.7 years ago by
serpalma.v
▴ 80
0
votes
3
replies
1.4k
views
Interpretation of full LD between extremely distant SNPs
linkage disequilibrium
SNP
updated 5.0 years ago by
Kevin Blighe
87k • written 5.0 years ago by
serpalma.v
▴ 80
1
vote
0
replies
2.1k
views
How to set the size of window for calculating Fst?
SNP
Fst
window
5.0 years ago by
serpalma.v
▴ 80
0
votes
0
replies
963
views
Scanning for selection using rehh2 from mouse WGS VCF
rehh2
sequencing
mouse
5.0 years ago by
serpalma.v
▴ 80
0
votes
0
replies
2.0k
views
How to detect outliers from either (a) SNP-Fst or (b) Window-Fst distributions?
Fst
vcftools
updated 5.1 years ago by
h.mon
35k • written 5.1 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.6k
views
Reference TiTv ratio for mouse WGS?
SNP
mouse
TiTv
Transition
Transversion
updated 5.1 years ago by
Biostar
20 • written 5.3 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.2k
views
Are both samtools mpileup options -m and -F only related to indel detection?
mpileup
samtools
next-gen
alignment
SNP
5.2 years ago by
serpalma.v
▴ 80
0
votes
2
replies
1.1k
views
How to select SNPs the most conservative way after WGS Variant Calling?
SNP
sequencing
next-gen
updated 5.2 years ago by
Istvan Albert
100k • written 5.2 years ago by
serpalma.v
▴ 80
0
votes
4
replies
4.8k
views
Overrepresented stretches of Gs in NovaSeq library
fastqc
sequencing
DNA
updated 5.3 years ago by
michael.ante
★ 3.8k • written 5.3 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.2k
views
History of the mouse genome
mouse
genome
sequencing
updated 5.3 years ago by
Biostar
20 • written 5.4 years ago by
serpalma.v
▴ 80
2
votes
5
replies
3.5k
views
bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
bcftools
samtools
mpileup
WGS
snp
5.4 years ago by
serpalma.v
▴ 80
0
votes
6
replies
2.2k
views
Per base GC content with a shoulder after adapter removal and trimming
fastqc
GC content
5.6 years ago by
serpalma.v
▴ 80
1
vote
4
replies
2.7k
views
Adding read group to bam files from multiplexed samples
bam
picard
gatk
updated 5.6 years ago by
Biostar
20 • written 5.8 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.9k
views
Discrepancy in gene set size between gage() and geneData()
gage
pathview
kegg
pathway analysis
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
serpalma.v
▴ 80
1
vote
3
replies
1.3k
views
what is the conventional apporach to calculate depth of coverage?
coverage
SNP
WGS
dnaseq
depth
updated 5.6 years ago by
finswimmer
16k • written 5.6 years ago by
serpalma.v
▴ 80
0
votes
9
replies
2.2k
views
Which indication of a failure can be found in bwa-mem or samtools' output?
bwa
samtools
updated 5.7 years ago by
ATpoint
82k • written 5.7 years ago by
serpalma.v
▴ 80
0
votes
2
replies
3.6k
views
Fix per tile sequence quality?
fastqc
DNAseq
illumina
quality control
updated 5.8 years ago by
GenoMax
141k • written 5.8 years ago by
serpalma.v
▴ 80
0
votes
1
reply
2.6k
views
kmer content changes after trimming and removing adapters from reads
DNAseq
trimmomatic
fastqc
5.8 years ago by
serpalma.v
▴ 80
4
votes
2
replies
7.0k
views
Removing Illumina Single End PCR Primers and TruSeq Adapters
DNA-seq
primer
TruSeq
adapter removal
FastQC
updated 5.9 years ago by
GenoMax
141k • written 5.9 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.0k
views
Recomendations on setting a software pipeline to detect signatures of selection
sweep
positive selection
signatures of selection
6.1 years ago by
serpalma.v
▴ 80
0
votes
2
replies
1.7k
views
Differences in RNAseq Variant Calling and Allele Specific Expression
RNA-Seq
variant calling
allele specific expression
updated 13 months ago by
afei
• 0 • written 6.2 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.6k
views
Calling ASE using QuASAR without availble population allele frequency
Allele specific expression
SNP
VCF
MAF
updated 6.4 years ago by
Biostar
20 • written 6.5 years ago by
serpalma.v
▴ 80
2
votes
1
reply
1.5k
views
How to find unique mappability regions in the bovine genome?
SNP
cow
Assembly
updated 6.5 years ago by
Pierre Lindenbaum
161k • written 6.5 years ago by
serpalma.v
▴ 80
2
votes
1
reply
1.7k
views
WASP criterion for discarding reads in unphased samples
WASP
RNA-Seq
allele-specific expression
6.5 years ago by
serpalma.v
▴ 80
2
votes
2
replies
1.3k
views
SNP annotated outside gene location (Variant Effect Predictor)
vep
SNP
variant effect predictor
ensembl
updated 6.7 years ago by
Denise CS
★ 5.2k • written 6.7 years ago by
serpalma.v
▴ 80
4
votes
5
replies
2.0k
views
Feasible Annotation of 4 million unique SNPs
SNP
ASE
GATK
updated 6.8 years ago by
Emily
23k • written 6.8 years ago by
serpalma.v
▴ 80
0
votes
1
reply
1.5k
views
Chromosome Names in genome are incompatible with annotations
STAR
alignment
7.1 years ago by
serpalma.v
▴ 80
0
votes
3
replies
4.0k
views
basic concepts behind --sjdbOverhang (STAR)
star
sjdbOverhang
7.1 years ago by
serpalma.v
▴ 80
0
votes
3
replies
1.3k
views
How to project the read count?(HiSeq2500, mouse genome, resequencing)
SNP
genome
sequence
next-gen
sequencing
updated 7.8 years ago by
GenoMax
141k • written 7.8 years ago by
serpalma.v
▴ 80
0
votes
2
replies
1.2k
views
Assigning time to data analysis (detection of signatures of selection)
SNP
sequencing
next-gen
7.8 years ago by
serpalma.v
▴ 80
1
vote
2
replies
1.7k
views
What is the language of this mass spectrophotometry data processing output file
mass spectrophotometry
output
updated 8.0 years ago by
Pierre Lindenbaum
161k • written 8.0 years ago by
serpalma.v
▴ 80
2
votes
2
replies
5.2k
views
Exploratory data anaylsis to detect batch effects
batch-effect
microarray
updated 20 months ago by
Ram
43k • written 8.4 years ago by
serpalma.v
▴ 80
0
votes
2
replies
1.9k
views
What test to apply to detect genomic signatures of selection?
genetics
selection
signatures
population-genomics
updated 21 months ago by
Ram
43k • written 8.3 years ago by
serpalma.v
▴ 80
0
votes
0
replies
1.4k
views
Find gene IDs for affymetrix chip pd.porgene.1.1.st
microarray
updated 2.6 years ago by
Ram
43k • written 8.4 years ago by
serpalma.v
▴ 80
0
votes
1
reply
3.1k
views
How to interpret a pairwise distance matrices for X nr-SNPs sliding windows across the genome
SNP
sliding-window
updated 20 months ago by
Ram
43k • written 8.5 years ago by
serpalma.v
▴ 80
1
vote
2
replies
5.8k
views
topGO approach for a list a genes without expression
GO
bioconductor
R
mirna
updated 3.1 years ago by
Ram
43k • written 9.5 years ago by
serpalma.v
▴ 80
3
votes
5
replies
3.5k
views
Max Length With Fastx Tookit
fastx
length
updated 10.4 years ago by
Istvan Albert
100k • written 10.4 years ago by
serpalma.v
▴ 80
0
votes
0
replies
6.0k
views
P1 And A Adater Trimming And Mapping From Ion Torrent Reads
ion-torrent
trimming
10.4 years ago by
serpalma.v
▴ 80
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