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115,829 results • Page
1 of 2317
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adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated just now by
lcj34
▴ 390 • written 3 hours ago by
b.contreras.moreira
▴ 10
0
votes
0
replies
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
2
replies
225
views
Ribo and RNA seq analysis
RNA-seq
genomics
Ribo-seq
updated 1 hour ago by
Jack Tierney
▴ 350 • written 25 days ago by
Manu Ayllon
• 0
0
votes
0
replies
15
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
14
views
Resources regarding Proteomics (In-Silico)
proteomics
protein
molecular
simulation
docking
1 hour ago by
Saurabh
• 0
0
votes
0
replies
23
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
30
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
2 hours ago by
Paula
• 0
791
votes
167
replies
138k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.5k • written 7.3 years ago by
Istvan Albert
100k
0
votes
2
replies
156
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
2 hours ago by
Learner
• 0
2
votes
1
reply
100
views
why there is an asterisk symbol at the end of each proteins sequences offasta files in the Braker3 output FASTA file?
gtf
breaker3
protein-seq
updated 52 minutes ago by
colindaven
6.2k • written 3 hours ago by
mathavanbioinfo
▴ 80
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
0
votes
2
replies
148
views
Beagle Phasing and Imputation
imputation
phasing
beagle
4 hours ago by
Duarte Molha
▴ 240
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
2
replies
132
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 4 hours ago by
fracarb8
★ 1.5k • written 14 hours ago by
bgbs
• 0
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 5 hours ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
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
2
replies
98
views
DEG (Differential expression gene) analysis
DEG
R
updated 5 hours ago by
dsull
★ 5.6k • written 6 hours ago by
sooni
▴ 20
0
votes
1
reply
110
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 6 hours ago by
Zhenyu Zhang
★ 1.1k • written 17 hours ago by
kcarey
• 0
0
votes
0
replies
44
views
News:
Online course: Adaptation Genomics
StructuralVariants
Selection
AdaptationGenomics
PopulationStructure
7 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
41
views
News:
Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics
Pangenomics
7 hours ago by
carlopecoraro2
★ 2.4k
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
1
reply
167
views
Is it better to pool samples prior to running deseq2, or should the algorithm be run separately for every pool?
deseq2
RNA-seq
updated 10 hours ago by
swbarnes2
14k • written 13 hours ago by
Shelby
• 0
0
votes
4
replies
228
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 10 hours ago by
Doomhammer
• 0 • written 1 day ago by
ben@f
▴ 10
0
votes
1
reply
498
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 11 hours ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
4
votes
4
replies
210
views
Differential express genes in imbalance groups
Limma
12 hours ago by
Chris
▴ 260
2
votes
1
reply
107
views
basal gene expression level
RNA-Seq
updated 16 hours ago by
LChart
3.8k • written 17 hours ago by
Francois Piumi
▴ 40
0
votes
0
replies
66
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
17 hours ago by
mhale
• 0
1
vote
1
reply
130
views
Seurat 5 integration
integration
seurat
updated 17 hours ago by
jared.andrews07
★ 16k • written 20 hours ago by
sarahmanderni
▴ 100
3
votes
5
replies
232
views
scRNAseq normalization
scRNA-seq
SCT
updated 3 hours ago by
ATpoint
81k • written 18 hours ago by
sarahmanderni
▴ 100
3
votes
7
replies
1.2k
views
7 follow
Transcription Start Site
TSS
updated 10 hours ago by
Ming Tommy Tang
★ 3.8k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
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
69
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
4
votes
2
replies
139
views
Problem with .bed file
cygwin64
bed
PLINK
updated 17 hours ago by
Ram
43k • written 21 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
178
views
compareCluster's enrichGO difference in results when stating ont = "ALL" vs NULL
enrichGO
clusterProfiler
updated 22 hours ago by
Dunois
★ 2.5k • written 1 day ago by
TIANTHING JESTLIN
• 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
4
votes
2
replies
245
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
7 hours ago by
경준
▴ 20
1
vote
2
replies
244
views
Trim Galore: Automatic detection of adapters
trimgalore
16 hours ago by
Daniel
▴ 30
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
4
replies
233
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 20 hours ago by
SequenceServer
▴ 140 • written 1 day ago by
Luca
• 0
0
votes
2
replies
159
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
21 hours ago by
Filip
• 0
1
vote
1
reply
112
views
turning old shell ncbi querys into url querys
eutils
ncbi
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Guelakais
• 0
0
votes
1
reply
456
views
ArchR Doublet Inference to Signac
Signac
scATAC-seq
ArchR
updated 1 day ago by
fracarb8
★ 1.5k • written 13 months ago by
bioinformatics.girl
▴ 20
0
votes
2
replies
159
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
1 day ago by
Niharika
• 0
3
votes
10
replies
631
views
t-test in two groups, multiple rows
R
t-test
13 hours ago by
sooni
▴ 20
3
votes
4
replies
1.3k
views
sam.gz files to bam using samtools
RNA-Seq
samtools
updated 1 day ago by
robertoalbanese.bioinfo
• 0 • written 12 months ago by
tikshyadav19
• 0
0
votes
4
replies
223
views
error in wigToBigWig while converting mappability to bedgraph
mappability
gem
bedgraph
wigToBigWig
4 hours ago by
Dora
▴ 10
115,829 results • Page
1 of 2317
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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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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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