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266 results • Page
1 of 6
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Views
Votes
Replies
0
votes
0
replies
12
views
A method to find if a variant is Genomic or an RNA-Editing variant
Editing
RNA-Seq
WES
RNA
Variant
1 hour ago by
hkarakurt
▴ 150
0
votes
0
replies
18
views
BEDOPS convert2bed output
vcf
bedops
convert2bed
bed
2 hours ago by
nehaklkn
• 0
1
vote
0
replies
35
views
Modelling vs removing effects from confounding variables and their uses for downstream analyses in RNA-seq experiments
removebatcheffect
sva
heatmap
plot
limma
pca
2 hours ago by
Jasmin
▴ 10
0
votes
0
replies
33
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
4 hours ago by
O.rka
▴ 610
0
votes
0
replies
29
views
Finding Specific Types of Data for Cancer Studies
TCGA
GDC
Cancer
Entrez
GEO
5 hours ago by
Vincent Laufer
★ 2.2k
0
votes
0
replies
57
views
Should the repressor really have a negative correlation with its motif?
atac-seq
scatac-seq
single-cell
4 hours ago by
Janus
• 0
1
vote
0
replies
55
views
How does LUMPY report breakpoints in multiple samples?
lumpy
SV
breakpoint
variation
structural
SVs
9 hours ago by
Getting there
▴ 80
2
votes
2
replies
102
views
Reference counts for RNA-seq
expression
rna
rna-seq
tpm
transcripts
updated 1 hour ago by
Giovanni M Dall'Olio
27k • written 17 hours ago by
syntax
▴ 70
0
votes
1
reply
66
views
Time Treatment analysis on Rna-Seq
R
GEO
Rna-seq
updated 18 hours ago by
Matthias Zepper
★ 1.4k • written 19 hours ago by
ShowPow
▴ 20
1
vote
0
replies
47
views
KissDE and batch effect
kissDE
kissplice
19 hours ago by
david.b.rombaut
▴ 10
0
votes
0
replies
50
views
Zenodo command line uploads
zenodo
updated 19 hours ago by
GenoMax
118k • written 20 hours ago by
zhousun21
▴ 40
0
votes
0
replies
54
views
Cytoscape visualisation issue
cytoscape
21 hours ago by
sarah.laverty20
• 0
0
votes
3
replies
118
views
CD4+ and CD8+ T cell classification
Immunology
T
cell
updated 20 hours ago by
antonioggsousa
★ 2.5k • written 23 hours ago by
pgangaitkar
• 0
0
votes
0
replies
59
views
filtering exonic variants from the annoated file
Filtering
snpEff
annotation
1 day ago by
maajid
• 0
0
votes
0
replies
64
views
Create UPGMA tree
TREE
SNP
UPGMA
R
GDS
1 day ago by
rjsgur789
• 0
0
votes
1
reply
81
views
Converting RSIDs in the HLA region (e.g.) HLA-A*:01:01g-B*08:01 format?
SNP
HLA
rsid
updated 20 hours ago by
GenoMax
118k • written 1 day ago by
4galaxy77
★ 2.2k
0
votes
0
replies
77
views
Signac peak sorting
scATAC-seq
seurat
signac
1 day ago by
rbronste
▴ 400
0
votes
0
replies
56
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 19 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
96
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
59
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
18 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
264
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 1 day 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
▴ 830 • 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
173
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
128
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
long
aligning
lastz
3 days ago by
vahe.galstyan
• 0
266 results • Page
1 of 6
Recent Votes
Answer: extracting sequences from a bam file
Answer: Genome-wide enrichment of histone marks and correlation with gene expression: Ap
Answer: Distinguishing records for reads in a pair in a SAM file
Answer: Distinguishing records for reads in a pair in a SAM file
A: How To Merge Cuffdiff Results To Make A Big Table?
Reference counts for RNA-seq
Comment: Reference counts for RNA-seq
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Recent Replies
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…
Comment: About normalization of the datasets from Harmonized TCGA data
by
qiz218591
▴ 10
How to validate that the data is already normalized? Is there any code or methods to validate? For example, you have said for the library s…
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
Vincent Laufer
★ 2.2k
Looks like i may want something like this (piping thru efetch): esearch -db gene -query "BRCA2 [GENE] AND human [ORGN]" |. efetch -format…
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
Vincent Laufer
★ 2.2k
suppose i wish to start from an amino acid position insteead, but then still pull nucleotides (or vice versa). Is there anyway to grab var…
Answer: How to check fastq file for feature retained from vector construct after RNA-seq
by
Zhenyu Zhang
▴ 560
All GenoMax said. Or you can align your reads to a reference genome that only contains your plasmid sequence
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