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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
23
views
BEDOPS convert2bed output
vcf
bedops
convert2bed
bed
2 hours ago by
nehaklkn
• 0
0
votes
0
replies
35
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
5 hours ago by
O.rka
▴ 610
0
votes
0
replies
31
views
Finding Specific Types of Data for Cancer Studies
TCGA
GDC
Cancer
Entrez
GEO
6 hours ago by
Vincent Laufer
★ 2.2k
0
votes
0
replies
61
views
Should the repressor really have a negative correlation with its motif?
atac-seq
scatac-seq
single-cell
5 hours ago by
Janus
• 0
1
vote
0
replies
56
views
How does LUMPY report breakpoints in multiple samples?
lumpy
SV
breakpoint
variation
structural
SVs
10 hours ago by
Getting there
▴ 80
2
votes
2
replies
105
views
Reference counts for RNA-seq
expression
rna
rna-seq
tpm
transcripts
updated 2 hours ago by
Giovanni M Dall'Olio
27k • written 18 hours ago by
syntax
▴ 70
0
votes
1
reply
68
views
Time Treatment analysis on Rna-Seq
R
GEO
Rna-seq
updated 19 hours ago by
Matthias Zepper
★ 1.4k • written 19 hours ago by
ShowPow
▴ 20
1
vote
0
replies
49
views
KissDE and batch effect
kissDE
kissplice
20 hours ago by
david.b.rombaut
▴ 10
0
votes
0
replies
52
views
Zenodo command line uploads
zenodo
updated 20 hours ago by
GenoMax
118k • written 21 hours ago by
zhousun21
▴ 40
0
votes
0
replies
56
views
Cytoscape visualisation issue
cytoscape
22 hours ago by
sarah.laverty20
• 0
0
votes
3
replies
120
views
CD4+ and CD8+ T cell classification
Immunology
T
cell
updated 21 hours ago by
antonioggsousa
★ 2.5k • written 1 day ago by
pgangaitkar
• 0
0
votes
0
replies
61
views
filtering exonic variants from the annoated file
Filtering
snpEff
annotation
1 day ago by
maajid
• 0
0
votes
0
replies
66
views
Create UPGMA tree
TREE
SNP
UPGMA
R
GDS
1 day ago by
rjsgur789
• 0
0
votes
1
reply
83
views
Converting RSIDs in the HLA region (e.g.) HLA-A*:01:01g-B*08:01 format?
SNP
HLA
rsid
updated 21 hours ago by
GenoMax
118k • written 1 day ago by
4galaxy77
★ 2.2k
0
votes
0
replies
79
views
Signac peak sorting
scATAC-seq
seurat
signac
1 day ago by
rbronste
▴ 400
0
votes
0
replies
58
views
cgMLST
MLST
1 day ago by
Ahmed Allam
• 0
0
votes
0
replies
74
views
checking allelic expression from SNP showing both Biallelic and monoallelic expression for sample gene
Single-Cell-RNA-seq
SNP
RNA-Seq
ASEreadcounter
allelic
1 day ago by
luckysardar171
▴ 20
0
votes
5
replies
216
views
GATK's selectVariants not outputting VCF
GATK
updated 20 hours ago by
Pierre Lindenbaum
147k • written 1 day ago by
dec986
▴ 340
0
votes
0
replies
96
views
inquiry related to gtex normalization
gtex
normalization
gene
count
1 day ago by
rheab1230
▴ 60
0
votes
0
replies
101
views
snpEff problems adding regulatory regions to database
snp
snpEff
gwas
TFBS
1 day ago by
mcsimenc
▴ 20
2
votes
0
replies
94
views
Composition-Conditioned-CrystalGAN
gans
proteinstructure
proteinfolding
pytorch
1 day ago by
Wiktoria
▴ 20
0
votes
1
reply
116
views
SQL query to find all specific value in all columns based on row id.
sql
updated 1 day ago by
Pierre Lindenbaum
147k • written 1 day ago by
lippithakkar
• 0
0
votes
0
replies
86
views
Signac MACS2 peak shape question
snATAC-seq
snRNA-seq
signac
multiome
seurat
1 day ago by
rbronste
▴ 400
0
votes
0
replies
69
views
D-loop in mitogenomes?
gene
genome
protein
1 day ago by
sunnykevin97
▴ 970
0
votes
0
replies
67
views
PennCNV-Seq
command
PennCNV-Seq
execute
the
1 day ago by
heureuse
• 0
1
vote
1
reply
97
views
Downloading Data from ICGC via Amazon AWS EC2
ICGC
Token
updated 1 day ago by
GenoMax
118k • written 1 day ago by
Hashirama
▴ 20
0
votes
0
replies
64
views
ASCAT + ShallowHRD
using
status
HRD
ShallowHRD
1 day ago by
shounak.chakraborty1990
▴ 20
0
votes
0
replies
60
views
Classify unknown TEs produced by RepeatModeler
repeats
TE
genome
1 day ago by
kirillkirilenko.tomsk
• 0
0
votes
2
replies
130
views
phylogeny
phylogeny
genes
with
virulence
19 hours ago by
saifulislam99121
• 0
0
votes
0
replies
71
views
Download specific sequences from databases using a Ruby-Script
KEGG
Ruby
database
2 days ago by
Theresa
• 0
0
votes
0
replies
76
views
facing difficulty while interpreting mean-variance trend plot in GEO2R
GEO2R
normalization
mean-variance
GEO
2 days ago by
ElfoHelpo
• 0
0
votes
0
replies
63
views
Fetching schemes from pubMLST
Fetching
pubMLST
schemes
cgMLST
scheme
2 days ago by
davidmaimoun
▴ 50
0
votes
1
reply
95
views
liftover bed not matching panel gene names
liftover
vcf
bed
bedtools
2 days ago by
whb
▴ 30
0
votes
3
replies
265
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
normalization
batcheffect
single_cell_features
training_test_split
1 day ago by
mmitra
▴ 40
0
votes
1
reply
150
views
STAR fails: quality string length is not equal to sequence length but only AFTER cutadapt is run
fastq
cutadapt
rna-seq
STAR
updated 2 days ago by
ATpoint
64k • written 2 days ago by
bioinfo_cat
• 0
0
votes
0
replies
95
views
UK Biobank vs. NIH-EBI GWAS catalogue
UK
Biobank
GWAS
NIH-EBI
2 days ago by
Sanjar
▴ 140
0
votes
4
replies
216
views
CPTAC data download, transcriptomics
CPTAC
download
data
transcriptome
1 day ago by
Rob
▴ 130
1
vote
1
reply
135
views
Determining strandedness of RNAseq samples from count data and understanding counts in sex genes
strandedness
htseq
RNAseq
updated 2 days ago by
ATpoint
64k • written 2 days ago by
sr41489
• 0
0
votes
1
reply
118
views
VCF to MAF using oncotator
vcf
maf
oncotator
to
updated 1 day ago by
Dave Carlson
▴ 840 • written 2 days ago by
hamrejr
• 0
0
votes
0
replies
81
views
How can one identify genome segments and mutations in Influenza viruses?
Bioinformatics
influenza
viruses
2 days ago by
eennadi
▴ 20
0
votes
0
replies
92
views
One-to-many pairwise alignment
pairwise
alignment
3 days ago by
Xiaokang
▴ 70
0
votes
0
replies
174
views
How to analyse .cdf or .mzML raw mass spectrometry files to get relative abundances of compounds in metabolome?
mass
spectrometry
data
metabolome
analysis
3 days ago by
dpc
▴ 240
1
vote
0
replies
101
views
r package for downstream analysis of phylogenetic trees
phylogenetics
R
3 days ago by
TM
▴ 10
0
votes
0
replies
93
views
any way to merge functions of kegg orthologs database?
functional-profile
metagenomics
data-wrangling
3 days ago by
v.berriosfarias
▴ 50
0
votes
0
replies
134
views
Package suggestion to calculate Protein-Protein interaction.
Free
FoldX
Binding
Affinity
Interaction
Energy
Protein-Protein
3 days ago by
UGUR
• 0
0
votes
1
reply
190
views
What does adjusted p value mean in GO overrepresentation analysis? [clusterProfiler]
clusterProfiler
updated 3 days ago by
4galaxy77
★ 2.2k • written 3 days ago by
Deepblue
▴ 10
0
votes
1
reply
140
views
Variant Effect Predictor (VEP) warning on insertions: coordinates are not (start = end + 1)
VCF
VEP
updated 3 days ago by
Pierre Lindenbaum
147k • written 3 days ago by
beketamas
• 0
0
votes
0
replies
130
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
long
aligning
lastz
3 days ago by
vahe.galstyan
• 0
0
votes
0
replies
106
views
exploring genetic differences among highly close populations
gene
snp
population
3 days ago by
yzko
• 0
0
votes
0
replies
109
views
Whole genome sequence data - plotting chromosome position in R -windows11?
data.
WGS
balance
allelic
plot
3 days ago by
H_variant1
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: How to split paired end SRA file into 2 correct fastq files
Answer: A method to find if a variant is Genomic or an RNA-Editing variant
Answer: Modelling vs removing effects from confounding variables and their uses for down
A: stringtie Error: input file cannot be found
Comment: AF = 0.5 in chrX, VCF of a male
Comment: AF = 0.5 in chrX, VCF of a male
Answer: extracting sequences from a bam file
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Recent Replies
Comment: AF = 0.5 in chrX, VCF of a male
by
paolo
▴ 10
My calls for chrX are all in the region between PAR1 and PAR2, so they are not in the pseudoautosomal region.
Answer: A method to find if a variant is Genomic or an RNA-Editing variant
by
i.sudbery
15k
No, not really. Not without access to matched DNA-sequencing form the same individual. [SPRINT][1] claims to be able to identify RNA ed…
Answer: Modelling vs removing effects from confounding variables and their uses for down
by
i.sudbery
15k
Confounders should be modeled where that is possible, not removed. This particularly applies to DE analysis, or anything that relies on cou…
Comment: WGCNA - problem with hclustplot (Human Chimp paper tutorial)
by
annamariabugaj
• 0
Thank you for the clarifying - yes, you are right, I can see the opposite expression levels in the top and bottom of Turquoise heatmap and …
Comment: Genome-wide enrichment of histone marks and correlation with gene expression: Ap
by
Ankit
▴ 350
Hi LChart, Thanks for the suggestions. IntePareto seems good option to start with. The others are machine learning based models which I am…
Comment: Distinguishing records for reads in a pair in a SAM file
by
appropiate
▴ 20
Thanks @d-cameron, yes, multiple alignments for R1 and R2 of the same template have the same name, and I only know how to distinguish if t…
Comment: Distinguishing records for reads in a pair in a SAM file
by
appropiate
▴ 20
Thanks a lot @dariober, you did understand correctly (I could have explained myself better...), just wanted to distinguish between first- a…
Comment: Reference counts for RNA-seq
by
Giovanni M Dall'Olio
27k
That's right, you cannot do DE without samples from the same experiment. At most, you can compare the top expressed genes against the [GTE…
Answer: How to match tumor fastq file to normal fastq file? (I just have a set of tumor
by
tomas4482
▴ 280
Check SRA selector runner for metadata, GEOdataset for metadata, original article for sampling tables or ask the authors. This is not a tec…
Comment: Are upset plots bad for differential expression analysis?
by
paulimer
▴ 10
That's really interesting! Majority vote is indeed a solution, provided I find an elegant way to settle ties. The app will always be used …
Comment: AF = 0.5 in chrX, VCF of a male
by
Pierre Lindenbaum
147k
a BAM is not perfect. If there is any region with a lot of mismatches (bad reads, duplicated regions, low complexity region...) , GATK will…
Answer: Distinguishing records for reads in a pair in a SAM file
by
dariober
13k
If I understand the question correctly, you want to know which of the multiple alignments are from the first-in-pair and which are from the…
Answer: Distinguishing records for reads in a pair in a SAM file
by
d-cameron
★ 2.6k
The [SAM file format specifications][1] states: Multiple mapping The correct placement of a read may be ambiguous, e.g., due to re…
Comment: AF = 0.5 in chrX, VCF of a male
by
d-cameron
★ 2.6k
Are these variants in the pseudoautosomal region?
Answer: Circos plot from SV data of WES samples
by
d-cameron
★ 2.6k
> I'm absolutely new in these waters so I'd very much appreciate some help. There are a number of issues that have the potentially to fund…
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