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Showing :
questions
2
votes
4
replies
540
views
VEP filtering query
ensembl-vep
3 months ago by
prasundutta87
▴ 660
1
vote
10
replies
1.2k
views
Coverage histogram query
Alignment
8 months ago by
prasundutta87
▴ 660
0
votes
2
replies
607
views
best practice to choose AF threshold based on population number
VCF
AF
allele-frequency
13 months ago by
prasundutta87
▴ 660
0
votes
0
replies
326
views
snpeff annotation query
snpeff
structural-variation
VCF
updated 14 months ago by
Ram
43k • written 14 months ago by
prasundutta87
▴ 660
0
votes
2
replies
875
views
alternate allele frequency and minor allele frequency
rare
common
SNV
SV
VCF
18 months ago by
prasundutta87
▴ 660
4
votes
11
replies
11k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
20 months ago by
prasundutta87
▴ 660
0
votes
0
replies
300
views
Tool for mode of inheritance based filtering for structural variants
StructuralVariants
genotypes
SNVs
trio
modeOfInheritance
2.1 years ago by
prasundutta87
▴ 660
2
votes
2
replies
2.9k
views
EPIC methylation manifest GRch38 query
methylation
coordinates
EPIC
bedgraph
CpG
updated 2.3 years ago by
Vincent
▴ 10 • written 3.9 years ago by
prasundutta87
▴ 660
0
votes
0
replies
421
views
query on filtering/dropping samples based on total reads (yield)
paired-end
fastq
Illumina
2.4 years ago by
prasundutta87
▴ 660
0
votes
1
reply
591
views
Structural variation nomenclature ambiguity
Structural_Variation
updated 2.6 years ago by
samuel.a.odonnell
▴ 520 • written 2.6 years ago by
prasundutta87
▴ 660
0
votes
2
replies
1.1k
views
Annotate Structural variants with population specific allele frequency values
allele
Structural_variation
VEP
frequency
VCF
2.6 years ago by
prasundutta87
▴ 660
3
votes
6
replies
1.4k
views
VEP chromosome name query
ensembl
VCF
annotation
VEP
2.9 years ago by
prasundutta87
▴ 660
0
votes
0
replies
518
views
About Structural variation genotypes
variants
Structural-variants
variant-calling
genotypes
updated 6 months ago by
Ram
43k • written 2.9 years ago by
prasundutta87
▴ 660
2
votes
2
replies
1.5k
views
bcftools norm resulting in '*' in alternate allele
SNP
bcftools
VCF
exome
3.2 years ago by
prasundutta87
▴ 660
1
vote
1
reply
1.3k
views
Using GRch38 (human genome) primary assembly for mapping long reads
assembly
alignment
updated 3.2 years ago by
colindaven
6.4k • written 3.2 years ago by
prasundutta87
▴ 660
0
votes
0
replies
446
views
number of reads outside exonic regions in an exome sequencing experiment
exome
next-gen
sequencing
3.2 years ago by
prasundutta87
▴ 660
0
votes
0
replies
877
views
Using 1000 genomes phase 3 variants for BQSR
SNP
next-gen
snp
GATK
3.3 years ago by
prasundutta87
▴ 660
4
votes
5
replies
842
views
Annotating variants using latest version fof the genome
SNP
snp
VCF
3.5 years ago by
prasundutta87
▴ 660
1
vote
1
reply
1.2k
views
rare SNP or SNV
snp
snv
3.7 years ago by
prasundutta87
▴ 660
0
votes
0
replies
702
views
find tabix version
tabix
software
VCF
3.7 years ago by
prasundutta87
▴ 660
0
votes
4
replies
950
views
methylation % calculation for targeted region
methylation
3.9 years ago by
prasundutta87
▴ 660
0
votes
2
replies
2.1k
views
query regarding using manifest and annotation in Minfi (EPIC Methylation array analysis)
R
Minfi
EPIC array
Methylation
updated 3.1 years ago by
lakshmibaskar
• 0 • written 4.0 years ago by
prasundutta87
▴ 660
1
vote
2
replies
767
views
array jobs accessing one binary in population genetics software
population genetics
software
SGE
updated 4.1 years ago by
ATpoint
82k • written 4.1 years ago by
prasundutta87
▴ 660
1
vote
10
replies
3.1k
views
illumina sequencing dual index query
sequencing
4.2 years ago by
prasundutta87
▴ 660
0
votes
1
reply
1.8k
views
soft-clipping during alignment and variant calling query
BWA-MEM
GATK
variant calling
alignment
updated 4.5 years ago by
Biostar
20 • written 4.5 years ago by
prasundutta87
▴ 660
0
votes
1
reply
1.7k
views
SnpEff using -onlyprotein option (meaning-Only use protein coding transcripts)
RNA-Seq
SNP
gene
software error
updated 4.5 years ago by
Mark
★ 1.5k • written 7.2 years ago by
prasundutta87
▴ 660
0
votes
0
replies
1.1k
views
candidate region selection in an XP-EHH analysis
SNP
XP-EHH
updated 4.7 years ago by
Biostar
20 • written 5.1 years ago by
prasundutta87
▴ 660
3
votes
3
replies
1.7k
views
allele specific expression (ASE) reference ratio plot query
RNA-Seq
allele-specific expression
SNP
4.9 years ago by
prasundutta87
▴ 660
1
vote
2
replies
2.7k
views
variant calling using reference transcriptome
RNA-Seq
SNP
reference transcriptome
updated 5.0 years ago by
eric.audemard
▴ 10 • written 7.2 years ago by
prasundutta87
▴ 660
0
votes
0
replies
1.0k
views
finding out SNPs from SNVs and breed specific SNPs
SNP
SNV
updated 5.0 years ago by
Biostar
20 • written 5.0 years ago by
prasundutta87
▴ 660
1
vote
2
replies
1.5k
views
outliers in XP-EHH
population genetics
outliers
XP-EHH
5.1 years ago by
prasundutta87
▴ 660
7
votes
5
replies
4.8k
views
Difference between Private SNPs and Singleton SNPs
SNPs
GATK
variant calling
SNP
population genetics
5.2 years ago by
prasundutta87
▴ 660
0
votes
0
replies
5.6k
views
Correct way to report variant statistics from bcftools stats report
SNP
variants statistics
bcftools
5.2 years ago by
prasundutta87
▴ 660
5
votes
3
replies
1.1k
views
some good practices doubts
alignment
gene
variant calling
updated 5.3 years ago by
Biostar
20 • written 6.5 years ago by
prasundutta87
▴ 660
4
votes
9
replies
2.2k
views
no gene_id for tRNA in GFF3
annotation
GFF3
GTF
5.5 years ago by
prasundutta87
▴ 660
0
votes
0
replies
1.1k
views
runtime error in LDhat
genome
snp
LDhat
population genetics
5.5 years ago by
prasundutta87
▴ 660
0
votes
6
replies
1.7k
views
Filtering results difference amongst VCF files
SNP
filtering
GATK
variants
5.6 years ago by
prasundutta87
▴ 660
0
votes
0
replies
1.5k
views
lookup table for LDhat
population genetics
ldhat
software
5.6 years ago by
prasundutta87
▴ 660
2
votes
2
replies
4.3k
views
PCA implementation in plink
Plink
PCA
population
updated 5.7 years ago by
chrchang523
10k • written 5.7 years ago by
prasundutta87
▴ 660
0
votes
2
replies
853
views
query on a pre-process step involving GFF3
GFF3
annotation
5.7 years ago by
prasundutta87
▴ 660
1
vote
2
replies
1.2k
views
some questions on GFF3
GFF
GTF
annotation
5.7 years ago by
prasundutta87
▴ 660
1
vote
2
replies
2.6k
views
gffread query for gff to gtf conversion
GFF
GTF
annotation
software
5.7 years ago by
prasundutta87
▴ 660
11
votes
5
replies
8.8k
views
HISAT2 MAPQ scoring scheme
alignment
5.8 years ago by
prasundutta87
▴ 660
0
votes
4
replies
934
views
sanity check methods for checking genome assembly coordinate changes
assembly
genome
sequence
5.8 years ago by
prasundutta87
▴ 660
3
votes
6
replies
1.2k
views
variant calling after reference genome is updated
SNP
variant calling
WGS
5.8 years ago by
prasundutta87
▴ 660
4
votes
14
replies
4.8k
views
Strategy in WGS variant calling using GATK (CombineGVCF step)
snp
variant calling
GATK
WGS
6.0 years ago by
prasundutta87
▴ 660
0
votes
4
replies
1.1k
views
addressing software versions
best practices
gatk
software error
6.2 years ago by
prasundutta87
▴ 660
8
votes
10
replies
12k
views
fastqc adapter content
sequencing
fastqc
quality control
updated 6.2 years ago by
GenoMax
142k • written 6.2 years ago by
prasundutta87
▴ 660
0
votes
3
replies
1.4k
views
heterozygosity during variant calling in a non-model organism such as Bubalus Bubalis
next-gen
sequencing
DNA-seq
SNP
6.3 years ago by
prasundutta87
▴ 660
0
votes
6
replies
2.3k
views
excessive loading time for VCF files in IGV
snp
visualization
IGV
6.5 years ago by
prasundutta87
▴ 660
63 results • Page
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