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Showing :
questions
2
votes
5
replies
1.4k
views
Assembling a sequence from the pairs of letters (X,Y)
R
sequence
updated 5.9 years ago by
zx8754
11k • written 5.9 years ago by
Bogdan
★ 1.4k
4
votes
10
replies
2.9k
views
filtering a VCF file based on genotype
VCF
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
1.2k
views
4C interaction analysis
4C
updated 6.0 years ago by
IP
▴ 760 • written 6.2 years ago by
Bogdan
★ 1.4k
0
votes
4
replies
1.2k
views
normalization when calling CNV areas on a genome-wide scale in tumor-germline samples
CNV
6.1 years ago by
Bogdan
★ 1.4k
6
votes
7
replies
1.6k
views
a realiable algorithm that calls INDELS of length 50bp-300bp in cancer genomes
INDEL
SNV
SV
CNV
updated 6.2 years ago by
Eric T.
★ 2.8k • written 6.2 years ago by
Bogdan
★ 1.4k
33
votes
26
replies
4.6k
views
7 follow
pathogenicity predictors of cancer mutations
cancer
pathogenicity
CADD
SIFT
POLYPHEN
updated 6.2 years ago by
onemoreuser
▴ 20 • written 6.5 years ago by
Bogdan
★ 1.4k
4
votes
3
replies
3.5k
views
about inversions: head-to-head and tail-to-tail
inversions
6.3 years ago by
Bogdan
★ 1.4k
4
votes
6
replies
1.6k
views
pipeline / workflow language
genome
updated 6.3 years ago by
Devon Ryan
104k • written 6.3 years ago by
Bogdan
★ 1.4k
1
vote
3
replies
1.7k
views
annotation of SV (structural variants)
SV
annotation
updated 6.3 years ago by
harishk0201
▴ 130 • written 6.3 years ago by
Bogdan
★ 1.4k
2
votes
4
replies
2.1k
views
computing the AF (allele fraction) for SV
SV
AF
structural variants
cancer genome
updated 6.4 years ago by
Biostar
20 • written 6.4 years ago by
Bogdan
★ 1.4k
9
votes
2
replies
2.8k
views
detecting LoH in cancer genomes
LOH
updated 6.4 years ago by
gaiusjaugustus
▴ 230 • written 6.4 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
1.9k
views
calling SV (or CNV) on CANCER SAMPLES with no GERMLINE
DELLY
LUMPY
MANTA
cn.mops
TitanCNA
6.4 years ago by
Bogdan
★ 1.4k
0
votes
2
replies
1.8k
views
normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
ChIP-Seq
edgeR
DESeq2
updated 6.5 years ago by
Carlo Yague
8.7k • written 6.7 years ago by
Bogdan
★ 1.4k
0
votes
5
replies
5.3k
views
extracting the exons coordinates on hg38
genome
exome
updated 6.6 years ago by
chen
★ 2.5k • written 6.6 years ago by
Bogdan
★ 1.4k
2
votes
4
replies
1.8k
views
CNV calling on tumor sample with no germline counterpart
CNV
updated 6.6 years ago by
Eric T.
★ 2.8k • written 6.6 years ago by
Bogdan
★ 1.4k
1
vote
4
replies
3.4k
views
calling the CNV in tumor-only samples (WGS and WES)
CNV
6.8 years ago by
Bogdan
★ 1.4k
8
votes
6
replies
2.6k
views
WES or WGS analysis of cancer samples with no matched germline
SNV
CNV
WGS
WES
updated 6.8 years ago by
markus.riester
▴ 550 • written 6.8 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
1.7k
views
about using cn.MOPS in detecting CNV in WES of germline-tumor samples
cn.MOPS
CNV
tumor
6.9 years ago by
Bogdan
★ 1.4k
6
votes
3
replies
2.5k
views
extracting the genes associated with the clusters
pheatmap
heatmap.2
complexheatmap
updated 7.1 years ago by
Biostar
20 • written 7.2 years ago by
Bogdan
★ 1.4k
4
votes
5
replies
3.6k
views
extracting Allele Read Counts
SNP
Titan
CNV
updated 7.1 years ago by
Pierre Lindenbaum
161k • written 7.1 years ago by
Bogdan
★ 1.4k
10
votes
6
replies
2.4k
views
somatic variant calling with no germline sample
SNP
indel
somatic mutation
updated 7.2 years ago by
d-cameron
★ 2.9k • written 7.2 years ago by
Bogdan
★ 1.4k
9
votes
2
replies
3.3k
views
filtering structural variants from normal-tumor pairs (whole-genome sequencing)
SV
LUMPY
DELLY
MANTA
filtering
updated 7.2 years ago by
d-cameron
★ 2.9k • written 7.2 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
1.3k
views
bias correction (an example from ChIP-seq)
ChIP-Seq
bias
correction
7.2 years ago by
Bogdan
★ 1.4k
5
votes
8
replies
5.5k
views
estimating tumor purity and ploidy and CNV
purity
ploidy
CNV
updated 7.2 years ago by
Eric T.
★ 2.8k • written 7.2 years ago by
Bogdan
★ 1.4k
9
votes
12
replies
2.1k
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
7.2 years ago by
Bogdan
★ 1.4k
3
votes
1
reply
2.3k
views
filtering the structural variants
SV
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
1.9k
views
calling deletions and duplications in the cancer genomes
genome
deletion
duplication
updated 7.3 years ago by
WouterDeCoster
47k • written 7.3 years ago by
Bogdan
★ 1.4k
3
votes
4
replies
2.0k
views
about computer memory and mpileup files
SNP
memory
varscan2
updated 7.6 years ago by
karl.stamm
4.1k • written 7.6 years ago by
Bogdan
★ 1.4k
8
votes
8
replies
5.2k
views
6 follow
CNV caller software
CNV
updated 7.6 years ago by
Lemire
▴ 940 • written 7.6 years ago by
Bogdan
★ 1.4k
9
votes
6
replies
3.3k
views
6 follow
Hi-C analysis and significant interactions
next-gen
updated 7.6 years ago by
Ashley Stephen Doane
▴ 20 • written 7.7 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
999
views
about multi-mapped reads and detection of chromosomal alterations
SNP
genome
7.6 years ago by
Bogdan
★ 1.4k
1
vote
2
replies
1.9k
views
about translocations in the cancer genomes
SNP
7.7 years ago by
Bogdan
★ 1.4k
3
votes
5
replies
3.3k
views
annotating a vcf file containing Structural Variants
SNP
snp
gene
updated 7.7 years ago by
igor
13k • written 7.7 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
1.5k
views
about the genome coordinates for mutations
SNP
8.0 years ago by
Bogdan
★ 1.4k
9
votes
4
replies
1.2k
views
winners in SMC (Somatic Mutation Challenge)
SNP
updated 8.0 years ago by
Chris Miller
22k • written 8.2 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
3.1k
views
about GATK VariantAnnotator and VCF files
VCF
updated 8.1 years ago by
Sean Davis
26k • written 8.1 years ago by
Bogdan
★ 1.4k
1
vote
3
replies
1.1k
views
about tools working on VCF and BAM files
SNP
8.1 years ago by
Bogdan
★ 1.4k
7
votes
21
replies
4.2k
views
about somatic mutation calling
SNP
genome
sequencing
snp
updated 8.1 years ago by
Tabea
▴ 30 • written 8.1 years ago by
Bogdan
★ 1.4k
3
votes
9
replies
3.8k
views
filtering VCF files
VCF
8.1 years ago by
Bogdan
★ 1.4k
1
vote
0
replies
1.4k
views
about adding MISSING fields TO VCF files
SNP
8.1 years ago by
Bogdan
★ 1.4k
2
votes
2
replies
1.9k
views
integrate vcf files
vcf
8.1 years ago by
Bogdan
★ 1.4k
2
votes
2
replies
1.4k
views
book on shell scripting
shell
8.1 years ago by
Bogdan
★ 1.4k
6
votes
16
replies
3.9k
views
about merging VCF files
vcf
SNP
8.1 years ago by
Bogdan
★ 1.4k
0
votes
2
replies
1.5k
views
mutation detection in tumors samples
SNP
sequencing
updated 8.2 years ago by
Chris Miller
22k • written 8.2 years ago by
Bogdan
★ 1.4k
2
votes
2
replies
3.0k
views
CPU/RAM resources for variant calling
SNP
next-gen
snp
8.2 years ago by
Bogdan
★ 1.4k
1
vote
6
replies
2.2k
views
about the use of varscan, somaticsnipper and samtools
sequencing
SNP
8.2 years ago by
Bogdan
★ 1.4k
50
votes
23
replies
24k
views
13 follow
intersect VCF files
VCF
updated 15 months ago by
Ram
43k • written 8.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
2.8k
views
running GATK or Mutect or a somatic variant caller individual chromosomes
sequencing
SNP
genome
updated 22 months ago by
Ram
43k • written 8.3 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
1.9k
views
SAM file and RNA-seq stranded/unstranded paired/unpaired
RNA-Seq
next-gen
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Bogdan
★ 1.4k
1
vote
3
replies
2.1k
views
linking GATK to MUTECT
GATK
8.4 years ago by
Bogdan
★ 1.4k
154 results • Page
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