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115,830 results • Page
1 of 2317
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Including reference genome in SNP-based phylogeny
reference
phylogeny
VCF
WGS
tree
just now by
maxrwjones
▴ 50
0
votes
1
reply
53
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
updated 16 minutes ago by
inedraylig
▴ 60 • written 4 hours ago by
samyu.senthil
• 0
0
votes
1
reply
50
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
updated 33 minutes ago by
Pierre Lindenbaum
160k • written 2 hours ago by
Марта
• 0
1
vote
1
reply
63
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 47 minutes ago by
lcj34
▴ 400 • written 4 hours ago by
b.contreras.moreira
▴ 10
0
votes
0
replies
17
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
1 hour ago by
b.contreras.moreira
▴ 10
0
votes
2
replies
233
views
Ribo and RNA seq analysis
RNA-seq
genomics
Ribo-seq
updated 2 hours ago by
Jack Tierney
▴ 350 • written 25 days ago by
Manu Ayllon
• 0
0
votes
0
replies
22
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
2 hours ago by
Bioinfo
▴ 20
1
vote
1
reply
42
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
updated 1 hour ago by
ATpoint
81k • written 2 hours ago by
sarahmanderni
▴ 100
0
votes
0
replies
32
views
Resources regarding Proteomics (In-Silico)
proteomics
protein
molecular
simulation
docking
2 hours ago by
Saurabh
• 0
0
votes
0
replies
40
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
169
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
3 hours ago by
Learner
• 0
3
votes
1
reply
127
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 1 hour ago by
colindaven
6.2k • written 3 hours ago by
mathavanbioinfo
▴ 80
0
votes
3
replies
185
views
Haddock 2.4
Protein
Docking
updated 1 hour ago by
dthorbur
★ 1.6k • written 1 day ago by
Preeti
• 0
0
votes
2
replies
150
views
Beagle Phasing and Imputation
imputation
phasing
beagle
5 hours ago by
Duarte Molha
▴ 240
1
vote
0
replies
39
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
5 hours ago by
marie.harmel
▴ 10
0
votes
2
replies
135
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 5 hours ago by
fracarb8
★ 1.5k • written 15 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
72
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq
GTEx
cram
updated 5 hours ago by
Pierre Lindenbaum
160k • written 6 hours ago by
Vullnet
• 0
0
votes
2
replies
104
views
DEG (Differential expression gene) analysis
DEG
R
updated 6 hours ago by
dsull
★ 5.6k • written 7 hours ago by
sooni
▴ 20
0
votes
1
reply
114
views
Biobambam vs Picard in RNA Sequencing Analysis for BAM to FASTQ
RNA-seq
Biobambam
Picard
updated 7 hours ago by
Zhenyu Zhang
★ 1.1k • written 17 hours ago by
kcarey
• 0
0
votes
0
replies
51
views
News:
Online course: Adaptation Genomics
StructuralVariants
Selection
AdaptationGenomics
PopulationStructure
7 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
47
views
News:
Online course: Analysis of Prokaryotic Pangenomes
BacterialGenomics
Pangenomics
8 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
72
views
library(scater)
sce
scRNASeq
scater
updated 9 hours ago by
Mensur Dlakic
★ 26k • written 9 hours ago by
Nitin
• 0
0
votes
1
reply
169
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 11 hours ago by
swbarnes2
14k • written 14 hours ago by
Shelby
• 0
0
votes
4
replies
230
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 11 hours ago by
Doomhammer
• 0 • written 1 day ago by
ben@f
▴ 10
0
votes
1
reply
499
views
Downloading epigenetic and mutation data of specific TCGA BRCA samples
Mutation
RNA-Seq
TCGA
updated 12 hours ago by
aUser
▴ 30 • written 2.6 years ago by
Soura
• 0
4
votes
4
replies
214
views
Differential express genes in imbalance groups
Limma
13 hours ago by
Chris
▴ 260
2
votes
1
reply
109
views
basal gene expression level
RNA-Seq
updated 17 hours ago by
LChart
3.8k • written 18 hours ago by
Francois Piumi
▴ 40
0
votes
0
replies
69
views
Evaluating MAST model fit using AIC
cell
single
MAST
scRNA
transcriptomics
17 hours ago by
mhale
• 0
1
vote
1
reply
132
views
Seurat 5 integration
integration
seurat
updated 18 hours ago by
jared.andrews07
★ 16k • written 21 hours ago by
sarahmanderni
▴ 100
3
votes
5
replies
240
views
scRNAseq normalization
scRNA-seq
SCT
updated 4 hours ago by
ATpoint
81k • written 19 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
74
views
Limma contrasts - difference between single and multiple concurrent contrasts results
R
limma
updated 20 hours ago by
Ram
43k • written 20 hours ago by
shasabhi1
• 0
0
votes
0
replies
77
views
Genotype simulation
gwas
simulation
sim1000
updated 21 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 21 hours ago by
Ram
43k • written 22 hours ago by
matt.a.bennett25890
• 0
4
votes
2
replies
141
views
Problem with .bed file
cygwin64
bed
PLINK
updated 18 hours ago by
Ram
43k • written 22 hours ago by
Dinmukhamed
• 0
0
votes
1
reply
179
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
78
views
Remove SNPs based on MAF in Fst analysis
SNP
MAF
Fst
Popgenome
23 hours ago by
kopelol
▴ 20
4
votes
2
replies
250
views
Before or after LD clumping for PRS calculation in GWAS
GWAS
7 hours ago by
경준
▴ 20
1
vote
2
replies
246
views
Trim Galore: Automatic detection of adapters
trimgalore
17 hours ago by
Daniel
▴ 30
1
vote
1
reply
126
views
Troubleshooting a REGENIE sex-stratified GWAS
GWAS
REGENIE
updated 4 hours ago by
Corentin
▴ 600 • written 1 day ago by
s.may-wilson
▴ 50
1
vote
3
replies
206
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
234
views
blastn: 2.2.31+ Package: blast 2.2.31, build Jun 2 2015 10:47:46
blastn
blast
ubuntu
updated 21 hours ago by
SequenceServer
▴ 140 • written 1 day ago by
Luca
• 0
0
votes
2
replies
160
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
22 hours ago by
Filip
• 0
1
vote
1
reply
113
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
457
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
160
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
1 day ago by
Niharika
• 0
3
votes
10
replies
633
views
t-test in two groups, multiple rows
R
t-test
14 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
115,830 results • Page
1 of 2317
Recent Votes
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
Error using -taxidlist blast
Error using -taxidlist blast
Answer: adding new assemblies to previously built practical haplotype graph (v2)
Comment: Single cluster spanning in different locations in UMAP in scRNAseq data
UniprotKB BLAST pipeline troubles
UniprotKB BLAST pipeline troubles
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Answer: Long branch lengths, low bootstrap values and misalignments
by
inedraylig
▴ 60
There's a lot of information missing from the question: what kind of data are you using? How was it obtained, aligned and filtered? A pipel…
Answer: How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
by
Pierre Lindenbaum
160k
using vcffilterjdk https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ ``` bcftools view in.vcf.gz |\ awk '/^#CHROM/ {printf("##FOR…
Answer: adding new assemblies to previously built practical haplotype graph (v2)
by
lcj34
▴ 400
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!
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