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1,000 results • Page
1 of 20
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0
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14
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
17 minutes ago by
b.contreras.moreira
▴ 10
0
votes
0
replies
17
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
1 hour ago by
Bioinfo
▴ 20
1
vote
1
reply
32
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
updated 54 minutes ago by
ATpoint
81k • written 1 hour ago by
sarahmanderni
▴ 100
0
votes
0
replies
16
views
Resources regarding Proteomics (In-Silico)
proteomics
protein
molecular
simulation
docking
1 hour ago by
Saurabh
• 0
0
votes
0
replies
24
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
1 hour ago by
Марта
• 0
0
votes
0
replies
32
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
2 hours ago by
Paula
• 0
0
votes
2
replies
156
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
2 hours ago by
Learner
• 0
0
votes
0
replies
28
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
3 hours ago by
samyu.senthil
• 0
0
votes
3
replies
177
views
Haddock 2.4
Protein
Docking
updated 34 minutes ago by
dthorbur
★ 1.6k • written 1 day ago by
Preeti
• 0
1
vote
0
replies
32
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
4 hours ago by
marie.harmel
▴ 10
0
votes
1
reply
68
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 5 hours ago by
Pierre Lindenbaum
160k • written 5 hours ago by
Vullnet
• 0
0
votes
1
reply
71
views
library(scater)
sce
scRNASeq
scater
updated 8 hours ago by
Mensur Dlakic
★ 26k • written 8 hours ago by
Nitin
• 0
0
votes
0
replies
68
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
17 hours ago by
mhale
• 0
0
votes
0
replies
73
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 19 hours ago by
Ram
43k • written 19 hours ago by
shasabhi1
• 0
0
votes
0
replies
75
views
Genotype simulation
gwas
simulation
sim1000
updated 20 hours ago by
Ram
43k • written 21 hours ago by
Eliza
▴ 30
0
votes
0
replies
71
views
Tabula Sapiens and scanpy normalised expression data
scanpy
scRNA-seq
10x
normalisation
updated 20 hours ago by
Ram
43k • written 21 hours ago by
matt.a.bennett25890
• 0
0
votes
0
replies
77
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
22 hours ago by
kopelol
▴ 20
1
vote
1
reply
119
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 3 hours ago by
Corentin
▴ 600 • written 1 day ago by
s.may-wilson
▴ 50
1
vote
3
replies
203
views
Average expression of a sample in single-cell data
single-cell
rna-seq
updated 10 hours ago by
dsull
★ 5.6k • written 1 day ago by
newuser2024
• 0
0
votes
2
replies
160
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
21 hours ago by
Filip
• 0
0
votes
2
replies
159
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
1 day ago by
Niharika
• 0
0
votes
2
replies
168
views
FASTA/FASTQ files of fetal Aneuploids
nipt
1 day ago by
lolbye_1
• 0
0
votes
0
replies
111
views
comparing sc-seq combination and bulk-sequencing
bulk-sequencing
sc-sequencing
1 day ago by
润达
• 0
0
votes
1
reply
149
views
BRIG coverage.graph issues
BRIG
sam
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
dlera.lozano
• 0
0
votes
0
replies
117
views
How to generate a comparative map using CGview?
genome
map
CGView
1 day ago by
marongiu.luigi
▴ 710
0
votes
0
replies
130
views
Advice on telling if two SNPs are on the same haplotype
ldpair
halplotype
co-occurance
gnomad
snp
2 days ago by
amy__
▴ 160
1
vote
2
replies
407
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
1 day ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
210
views
Upset plot
upsetplot
23 hours ago by
Chris
▴ 260
0
votes
1
reply
178
views
Are there any tools for mutational analysis of viruses?
virus
updated 21 hours ago by
Ram
43k • written 2 days ago by
joey
▴ 10
0
votes
1
reply
230
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
updated 2 days ago by
Arton
• 0 • written 5 days ago by
Samuel
▴ 20
0
votes
0
replies
122
views
Analyzing differentially methylated regions from Nanopore long read data?
bioinformatics
Long
read
sequencing
methylation
2 days ago by
Arton
• 0
1
vote
1
reply
167
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
updated 21 hours ago by
Ram
43k • written 2 days ago by
bioinfo_enthusiast
• 0
1
vote
0
replies
127
views
How should I regenotype VCFs using vg?
vg
2 days ago by
Ricky
▴ 10
1
vote
2
replies
215
views
What GC content should I expect?
RNA-seq
GC-content
updated 2 days ago by
ATpoint
81k • written 2 days ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
122
views
stat test
stattest
chi2
updated 2 days ago by
GenoMax
140k • written 2 days ago by
NLL
• 0
0
votes
0
replies
145
views
Anvio HMM source campbell_et_al
anvio
updated 21 hours ago by
Ram
43k • written 3 days ago by
Hayler Edu
▴ 40
0
votes
1
reply
205
views
Issue with bigWigSummary utility of Kent/UCSC utilities
bigWig
UCSC
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
eeb74
• 0
0
votes
1
reply
195
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
eeb74
• 0
1
vote
1
reply
219
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 3 days ago by
GenoMax
140k • written 3 days ago by
geocarvalho
▴ 360
0
votes
0
replies
143
views
admixfrog for high-coverage data
introgression
3 days ago by
gubrins
▴ 290
0
votes
1
reply
201
views
updateR() error
R
update
updated 1 day ago by
dthorbur
★ 1.6k • written 4 days ago by
marco.barr
▴ 30
0
votes
0
replies
143
views
Haplotype Phasing from Yeast strains
yeast
haplotype
phasing
4 days ago by
Sven K
• 0
0
votes
0
replies
159
views
cufflinks- cuffquant issue
cufflinks
4 days ago by
soyeon
• 0
2
votes
2
replies
242
views
compare dimplot(single cell)
DEG
scRNAseq
3 days ago by
kayah
• 0
1
vote
1
reply
210
views
--busco_db and --busco_seed_species with RNA-seq
RNA-seq
Funannotate
busco
4 days ago by
sansan_96
▴ 50
0
votes
0
replies
149
views
Computational Package to engage Type 2 Diabetes Knowledge Portal (T2DKP)
workflow
Package
4 days ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
180
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 4 days ago by
jared.andrews07
★ 16k • written 4 days ago by
PBC
▴ 10
1
vote
1
reply
196
views
lncRNA and ncPEPs identification
lncRNA
updated 4 days ago by
Yahel
• 0 • written 6 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
118
views
Music2 human to mouse deconvolution
deconvolution
liftover
music2
4 days ago by
rbronste
▴ 420
0
votes
2
replies
171
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
4 days ago by
njornet
▴ 10
1,000 results • Page
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Recent Votes
Comment: Single cluster spanning in different locations in UMAP in scRNAseq data
UniprotKB BLAST pipeline troubles
UniprotKB BLAST pipeline troubles
Comment: UniprotKB BLAST pipeline troubles
Answer: UniprotKB BLAST pipeline troubles
Cross-referencing Id from Swiss-Prot/UniProtKB human reference proteome to Ensembl Genes
Answer: Cross-referencing Id from Swiss-Prot/UniProtKB human reference proteome to Ensem
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Recent Replies
Answer: adding new assemblies to previously built practical haplotype graph (v2)
by
lcj34
▴ 390
Bruno: You can add new assemblies at any time. The vcfs are not dependent on one another. The only issue would be if you want to impute …
Comment: Haddock 2.4
by
dthorbur
★ 1.6k
You are only focusing on a single value. There are numerous descriptive statistics reported after a run. Together they describe the fit and…
Comment: Single cluster spanning in different locations in UMAP in scRNAseq data
by
ATpoint
81k
It means that there is a disagreement between UMAP and clustering algorithm, but since UMAP is mostly just visualization you could ignore i…
Comment: Ribo and RNA seq analysis
by
Jack Tierney
▴ 350
Hi Manu Ayllon, It is difficult to advise as I am unclear on the goal of your project. I will tell you what I understand and you can co…
Answer: Ribo and RNA seq analysis
by
Manu Ayllon
• 0
I got it making use of blastn, creating first a database with the RNA sequences and doing blast with the Ribo-seq sequences as query. The p…
Comment: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Comment: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
Corentin
▴ 600
Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Comment: Beagle Phasing and Imputation
by
Duarte Molha
▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
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