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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
210
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 10 days ago by
Jeremy
▴ 850 • written 10 days ago by
camillab.
▴ 150
0
votes
1
reply
172
views
WGCNA convenience function
WGCNA
updated 9 days ago by
andres.firrincieli
3.5k • written 10 days ago by
fluentin44
• 0
0
votes
0
replies
123
views
Low mapping after Cufflinks assembly
assembly
gffread
cuffmerge
Cufflinks
RSEM
10 days ago by
sofiablancoglez
• 0
0
votes
0
replies
117
views
KEGG module and abundance of its KEGG Orthologs for functioning
function
kegg
abundance
10 days ago by
Jonathan Yoou
▴ 60
1
vote
4
replies
286
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 10 days ago by
ATpoint
78k • written 10 days ago by
annaA
▴ 10
0
votes
0
replies
115
views
RNASeq vs TermSeq
RNAseq
statistics
TermSeq
10 days ago by
npb27
• 0
0
votes
0
replies
108
views
Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?
normalization
array
10 days ago by
rk.khayami94
▴ 10
0
votes
0
replies
115
views
Interpretation of mean-variance trend in voom
EdgeR
Voom
updated 10 days ago by
Ram
41k • written 10 days ago by
Ivana
• 0
0
votes
0
replies
169
views
How to perform analysis with given copy number variation datasets between disease and control cohorts
CNV
analysis
10 days ago by
Tsin-Lau
• 0
0
votes
0
replies
115
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview
KEGG
10 days ago by
B.N.
• 0
0
votes
3
replies
283
views
Jellyfish problem with Failed to open input file 'reads.jf'
jellyfish
kmer
fastq
9 days ago by
m.t.lorenc
• 0
0
votes
6
replies
509
views
Problem aligning target capture sequencing of a few hundred regions to the human reference genome
GATK4
bwa-mem
target-capture-sequencing
alignment
9 days ago by
Miguel
• 0
0
votes
0
replies
110
views
Ancestral Allele FASTA sequence aligned with Candidate Gene Region
Allele
GRSch38
Ancestral
FASTA
GRSch37
10 days ago by
Warrenkb
• 0
0
votes
3
replies
333
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 9 days ago by
MatthewP
★ 1.3k • written 11 days ago by
skinny_genes
• 0
0
votes
0
replies
144
views
Getting all the X associated genes of an organism
Rattus-norvegicus
neurobiology
updated 11 days ago by
Ram
41k • written 11 days ago by
Uri
• 0
0
votes
0
replies
123
views
coupling Cufflinks results with RSEM
transcript-level-quantification
RSEM
transcriptome-assembly
Cufflinks
11 days ago by
sofiablancoglez
• 0
4
votes
6
replies
390
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
11 days ago by
Tihana
▴ 10
2
votes
1
reply
156
views
Extract variants from 100 000 genomes project
variants
100000-genomes-project
updated 11 days ago by
Ram
41k • written 11 days ago by
Mairena
• 0
0
votes
0
replies
111
views
NA values in conumee detail
cnv
copy-number
conumee
updated 11 days ago by
Ram
41k • written 11 days ago by
sativus
▴ 10
1
vote
2
replies
261
views
How to remove batch effect in RNA-seq using control samples?
Batch-effect
RNA-seq
10 days ago by
AS20
▴ 10
0
votes
0
replies
109
views
Which of the following relationships is correct for making a hypothetical ceRNA?
cancer
lncRNA
ceRNA
RNA
miRNA
11 days ago by
mohammadhassanj
▴ 260
0
votes
0
replies
144
views
How to obtain full alignment results?
giraffe
vg
11 days ago by
nrqstudent
• 0
0
votes
1
reply
214
views
Seeking Advice on Validating RNA-Seq Data Before Differential Analysis
RNA-Seq
updated 12 days ago by
ATpoint
78k • written 12 days ago by
Tully
• 0
1
vote
1
reply
198
views
Model matrix confront 2 groups out of 3
modelmatrix
r
designformula
deseq2
drimseq
updated 12 days ago by
ATpoint
78k • written 12 days ago by
dylannicoembros
• 0
0
votes
0
replies
163
views
Extracting conserved sequences with clustralw
conservation
clustalw
updated 12 days ago by
Pierre Lindenbaum
158k • written 12 days ago by
iftikharmaryam123
• 0
0
votes
0
replies
171
views
TSSAR and TSSpredator
sRNA
TSS
13 days ago by
Sado
• 0
0
votes
7
replies
528
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 11 days ago by
Ram
41k • written 13 days ago by
George
• 0
0
votes
3
replies
397
views
percentage of cells in each cluster- Seurat
seurat
updated 11 days ago by
seidel
11k • written 14 days ago by
odi
▴ 10
0
votes
0
replies
198
views
PANTHER functional classification
PANTHER
Gene-Ontology
updated 14 days ago by
Ram
41k • written 14 days ago by
rls_08
▴ 40
0
votes
2
replies
318
views
How to perform liftover from 38 to 37 in R?
R
genomics
hail
liftover
gwas
13 days ago by
DN99
▴ 20
0
votes
0
replies
178
views
Circos error value
circos
14 days ago by
KiInga
• 0
0
votes
0
replies
177
views
beagle to gds for admixture mapping
admixture
genesis
gwastools
gds
beagle
14 days ago by
nanodano
▴ 30
0
votes
2
replies
257
views
error in determining minimum contigs in Velvet
contigs
terminal
velvet
14 days ago by
Kárita
• 0
2
votes
2
replies
299
views
DESeq2 installation failures
DEseq2
updated 12 days ago by
Michael
53k • written 14 days ago by
dantuluri
• 0
0
votes
0
replies
190
views
Seurat clustering results
seurat
UMAP
clustering
single-cell
14 days ago by
Kaia
• 0
0
votes
4
replies
576
views
WGCNA Analysis - blockwiseModules data processing
WGCNA
blockwiseModules
updated 14 days ago by
GenoMax
136k • written 3 months ago by
Raito92
▴ 90
1
vote
4
replies
375
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
14 days ago by
George
• 0
3
votes
4
replies
424
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
11 days ago by
QX
• 0
0
votes
0
replies
169
views
ripSeek error : no method or default for coercing “NULL” to “GRanges”
R
ripSeek
ripSeeker
RIP
14 days ago by
maria
• 0
1
vote
3
replies
319
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 14 days ago by
Ram
41k • written 14 days ago by
adarsh_pp
▴ 30
0
votes
0
replies
169
views
Help with coshing mutations for oncoplot
oncoplot
maftools
14 days ago by
Toni
• 0
0
votes
0
replies
170
views
Handling male samples chrX vcf genotype from 1000G high-coverage 30x
chrX
1000G
vcf
male
genotype
14 days ago by
Pau
• 0
0
votes
0
replies
166
views
Bedtools coverage -hist "all" in chr column
-hist
Coverage
option
breadth
Bedtools
14 days ago by
Smriti
▴ 10
0
votes
2
replies
265
views
UCSC Genome Browser Custom Track Blank
customtrack
UCSC
chipseq
14 days ago by
Daniel
▴ 30
0
votes
1
reply
220
views
Error with HTseq RNAseq read count
RNAseq
HTseq
updated 14 days ago by
GenoMax
136k • written 15 days ago by
Catalina
• 0
0
votes
4
replies
396
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
DiffBind
csaw
normalization
spikein
ChIPseq
14 days ago by
jared.andrews07
★ 16k
0
votes
2
replies
261
views
How to change "CompressedGRangesList" to "GRangesList"
liftOver
minfi
14 days ago by
Aki
▴ 10
0
votes
2
replies
251
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
1 day ago by
junli1988
• 0
0
votes
3
replies
322
views
RNA star taking more than 24h to complete 2nd pass
rna-seq
star
updated 15 days ago by
Ram
41k • written 15 days ago by
manuelmourato25
• 0
1
vote
1
reply
233
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
9 days ago by
Lukas
▴ 40
1,000 results • Page
3 of 20
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Recent Awards •
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Popular Question
to
beausoleilmo
▴ 560
Commentator
to
Brian Bushnell
19k
Popular Question
to
Gama313
▴ 120
Popular Question
to
nanodano
▴ 30
Popular Question
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shome
▴ 10
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Malachi Griffith
19k
Scholar
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jared.andrews07
★ 16k
Recent Replies
Comment: "MethylKit" package for WGBS data
by
viveksomya123
• 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat?
by
synat.keam
▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization
by
geneontologyhelp
▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements?
by
cmdcolin
★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations
by
Jordan M Eizenga
▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ?
by
Jordan M Eizenga
▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
Brian Bushnell
19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data
by
Tm
★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them?
by
Brian Bushnell
19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization
by
m.habib
• 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
jv
★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
by
Malachi Griffith
19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
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