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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
173
views
WGCNA convenience function
WGCNA
updated 10 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
287
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 11 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
11 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
10 days ago by
m.t.lorenc
• 0
0
votes
6
replies
512
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
11 days ago by
Warrenkb
• 0
0
votes
3
replies
334
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 10 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
392
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
112
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
11 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
12 days ago by
mohammadhassanj
▴ 260
0
votes
0
replies
144
views
How to obtain full alignment results?
giraffe
vg
12 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 13 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
529
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
398
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
199
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
319
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
179
views
Circos error value
circos
14 days ago by
KiInga
• 0
0
votes
0
replies
178
views
beagle to gds for admixture mapping
admixture
genesis
gwastools
gds
beagle
14 days ago by
nanodano
▴ 30
0
votes
2
replies
258
views
error in determining minimum contigs in Velvet
contigs
terminal
velvet
14 days ago by
Kárita
• 0
2
votes
2
replies
301
views
DESeq2 installation failures
DEseq2
updated 12 days ago by
Michael
53k • written 14 days ago by
dantuluri
• 0
0
votes
0
replies
192
views
Seurat clustering results
seurat
UMAP
clustering
single-cell
14 days ago by
Kaia
• 0
0
votes
4
replies
579
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
377
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
14 days ago by
George
• 0
3
votes
4
replies
427
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
12 days ago by
QX
• 0
0
votes
0
replies
170
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
320
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
170
views
Help with coshing mutations for oncoplot
oncoplot
maftools
14 days ago by
Toni
• 0
0
votes
0
replies
171
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
167
views
Bedtools coverage -hist "all" in chr column
-hist
Coverage
option
breadth
Bedtools
15 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
221
views
Error with HTseq RNAseq read count
RNAseq
HTseq
updated 15 days ago by
GenoMax
136k • written 15 days ago by
Catalina
• 0
0
votes
4
replies
397
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
262
views
How to change "CompressedGRangesList" to "GRangesList"
liftOver
minfi
14 days ago by
Aki
▴ 10
0
votes
2
replies
252
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
1 day ago by
junli1988
• 0
0
votes
3
replies
323
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
234
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
9 days ago by
Lukas
▴ 40
1,000 results • Page
3 of 20
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Recent Awards •
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Popular Question
to
seta
★ 1.8k
Popular Question
to
endre.sebestyen
▴ 10
Popular Question
to
beausoleilmo
▴ 560
Commentator
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Brian Bushnell
19k
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Gama313
▴ 120
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nanodano
▴ 30
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shome
▴ 10
Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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