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120,756 results • Page
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Olink - OlinkAnalyze Package - olink_umap_plot function
Olink
proteomics
just now by
kristina
• 0
0
votes
1
reply
6
views
bwa-mem keeps failing to locate the index files
bwa
bwa-mem
updated just now by
SIMONE
• 0 • written 6 minutes ago by
pairedttest
▴ 30
0
votes
0
replies
16
views
Herald:
The Biostar Herald for Wednesday, March 19, 2025
herald
1 hour ago by
Biostar
3.4k
4
votes
10
replies
109
views
prokka with too many "hypothetical proteins" and genome comparison
comparison
genome
galaxy
prokka
4 minutes ago by
avinci1
▴ 20
0
votes
0
replies
33
views
Cosmic database update issue in annovar
annovar
cosmic
genomics
updated 26 minutes ago by
Ram
45k • written 4 hours ago by
abhijitswain
• 0
1
vote
1
reply
204
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF
genotype
gVCF
4 hours ago by
Michaela
▴ 10
3
votes
11
replies
6.9k
views
11 follow
How to draw venn diagram for two CNV lists?
venn
updated 8 hours ago by
Aj
• 0 • written 10.3 years ago by
lyz10302012
▴ 470
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
47
views
Split paired ended hWGS FASTq files to simulate difference sequence coverage
whole-genome-sequencing
wgs
FASTQ
coverage
updated 21 minutes ago by
Ram
45k • written 8 hours ago by
DJBill
▴ 20
1
vote
2
replies
140
views
How do I figure out pangenome location of hg38 coordinates?
pangenome
hg38
vg
13 hours ago by
a5864557
• 0
1
vote
4
replies
182
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
gtf
curation
gene
updated 21 minutes ago by
Ram
45k • written 21 hours ago by
Esra
• 0
0
votes
0
replies
57
views
generating manhattan plot through hail
plot
manhattan
hail
visualizations
gwas
16 hours ago by
nitya
• 0
0
votes
0
replies
60
views
Hard Filtering Differences between WES and WGS
WES
WGS
Hard-Filtering
updated 24 minutes ago by
Ram
45k • written 17 hours ago by
SIMONE
• 0
0
votes
3
replies
132
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2
single-cell
pseudobulk
updated 2 hours ago by
ATpoint
87k • written 18 hours ago by
Aspire
▴ 370
0
votes
0
replies
74
views
OMA use case
oma
omastandalone
15 hours ago by
nmalexan
• 0
2
votes
4
replies
285
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 18 hours ago by
Istvan Albert
102k • written 2 days ago by
Megan
▴ 50
1
vote
3
replies
129
views
nanopore SNV callers returns empty VCF
snv_caller
nanopore
updated 1 hour ago by
Istvan Albert
102k • written 20 hours ago by
Meghan.T
• 0
13
votes
3
replies
1.0k
views
Tutorial:
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda
Anaconda
license
20 hours ago by
Juke34
9.1k
0
votes
1
reply
92
views
How many cells are needed in subcluster to draw conclusions?
immunology
T-cells
scRNA-seq
updated 5 hours ago by
ATpoint
87k • written 20 hours ago by
S
• 0
0
votes
1
reply
96
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
updated 18 hours ago by
Istvan Albert
102k • written 21 hours ago by
bioinfo
▴ 150
2
votes
2
replies
155
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria
rnaseq
adapter-trimming
6 hours ago by
Davor
• 0
1
vote
2
replies
159
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep
snpeff
updated 1 day ago by
Jeremy Leipzig
23k • written 1 day ago by
mary.v.volkova
▴ 20
0
votes
1
reply
77
views
How to plot LMER estimate values in heatmap ?
cell
scRNAseq
TF
lmer
transcription
updated 1 day ago by
ATpoint
87k • written 1 day ago by
carolofharvest
▴ 50
1
vote
2
replies
675
views
News:
Final Call - Next-Generation Sequencing Data Analysis: A Practical Introduction (April 2-4 in Munich) - Only 2 seats left
Workshop
RNAseq
Variant-Calling
Illumina
DNAseq
1 day ago by
ecSeq Bioinformatics
▴ 10
0
votes
1
reply
105
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates
DESeq2
RNA-Seq
updated 23 hours ago by
Ram
45k • written 1 day ago by
hellothere
• 0
0
votes
1
reply
102
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
bioinformatics
GWAS
genetics
WGS
updated 1 day ago by
Arup Ghosh
3.3k • written 1 day ago by
K
• 0
0
votes
1
reply
143
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
baibhu1234
▴ 40
0
votes
0
replies
98
views
Beagle Imputation
Beagle
Imputation
1 day ago by
mahlet.teka
• 0
0
votes
0
replies
215
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount
somaticsniper
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
1phamcha2
• 0
2
votes
2
replies
183
views
miRNA-seq: QC reports and workflow
miRNA-seq
ION-Torrent
RNA-seq
FASTQC
19 hours ago by
omicon
▴ 40
1
vote
0
replies
90
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans
Foldseek
Genes
Orthologs
Homologs
1 day ago by
bioinformatics_rk
▴ 10
0
votes
1
reply
175
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 1 day ago by
shelkmike
★ 1.5k • written 3 days ago by
Mark
▴ 30
0
votes
1
reply
152
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 1 day ago by
shelkmike
★ 1.5k • written 2 days ago by
Ariadna
▴ 20
3
votes
2
replies
211
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
1 day ago by
Riley J
• 0
2
votes
3
replies
190
views
Population genetics with mutect2 data
haplotypecaller
mutect2
updated 13 hours ago by
LauferVA
4.6k • written 2 days ago by
slzr_
• 0
1
vote
2
replies
153
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 2 days ago by
Watermelon
• 0 • written 2 days ago by
gogeni5529
▴ 60
1
vote
2
replies
186
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 1 day ago by
Ram
45k • written 2 days ago by
uttkarsh
• 0
0
votes
0
replies
96
views
Chrom3D
chrom3d
interchromosomal
genome
model
2 days ago by
desptsp
• 0
0
votes
1
reply
114
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
2 days ago by
ZheFrench
▴ 590
1
vote
3
replies
175
views
CPTAC Data analysis
CPTAC
proteomics
updated 2 days ago by
LauferVA
4.6k • written 2 days ago by
jain72744
▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere
ucsc
updated 1 day ago by
Ram
45k • written 14.5 years ago by
Jdk
▴ 260
0
votes
3
replies
167
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 2 days ago by
GenoMax
150k • written 2 days ago by
omicon
▴ 40
0
votes
3
replies
179
views
Methylation cpg probes annotation
annotation
methylation
cpg
TCGA
updated 2 days ago by
GenoMax
150k • written 2 days ago by
jain72744
▴ 10
1
vote
2
replies
286
views
How to convert .ab1 to fastq
Fastq
updated 2 days ago by
size_t
▴ 120 • written 4 days ago by
dr.suvarnakapale
• 0
1
vote
3
replies
199
views
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 2 days ago by
colindaven
7.3k • written 2 days ago by
Shuo
• 0
0
votes
1
reply
142
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
updated 2 days ago by
dthorbur
★ 2.9k • written 2 days ago by
v.berriosfarias
▴ 140
0
votes
1
reply
185
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
updated 2 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
179
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
1 day ago by
Jl
• 0
1
vote
2
replies
186
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
2 days ago by
noodlejackson
▴ 40
0
votes
0
replies
120
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
2 days ago by
emalekos
▴ 40
120,756 results • Page
1 of 2416
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Comment: prokka with too many "hypothetical proteins" and genome comparison
Comment: prokka with too many "hypothetical proteins" and genome comparison
NGS Data Storage Best Practices (Clinical)
Comment: Is there too little variation to detect meaningful gene changes?
Answer: Is there too little variation to detect meaningful gene changes?
prokka with too many "hypothetical proteins" and genome comparison
Comment: What are the advantages of using the T2T as a reference vs GRCh38 today?
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Answer: bwa-mem keeps failing to locate the index files
by
SIMONE
• 0
in my code the reference is .fasta, not .fa, i don't this could be the issue
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
▴ 20
I'm working with everything I have, to be honest. I will work with aa sequences and try MMseq2. Thank you so much for the help!
Comment: Analysing Microarray Data In Bioconductor
by
Riley J
• 0
Hi! Did you find it? I am struggling with gene expression meta-analysis, but don't know how to strat the analysis. Do you have any material…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
Dunois
★ 2.9k
Are you working with nucleotide sequences or amino acid sequences? It's best to perform all these kinds of sequence comparisons with the la…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
▴ 20
Thank you so much for your help. I don't know how usual is to have 50% of hypotetical proteins. If I have to give you a number they are aro…
Comment: nanopore SNV callers returns empty VCF
by
Istvan Albert
102k
it is very unlikely that the number of mutations caused the reads to fail to align. The number of mutations needed to cause that would be v…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
Joe
22k
What is the organism? 50% hypothetical isn't that crazy to me if its something a bit unusual. I spent my PhD working on a gene cluster wher…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
▴ 20
We tried to select the specific database for the bacteria, but the result was the same. All hypotetical proteins. At least half of the outp…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
Joe
22k
What do you mean there are too many? It is normal to encounter a lot of hypotheticals unless its a very well characterised organism. If it…
Comment: Am I accounting for replicates correctly in pseudobulk analysis?
by
ATpoint
87k
I would test the celltype and treatment effect here via the averages, for example for the celltype effect as below. I think that's one way …
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
▴ 20
Basically I sent the DNA of both bacteria to a sequencing service and they gave us the annotation files, with excel files, prokka annotatio…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
GenoMax
150k
What state are these genomes in? Single contig or multiple pieces. Were they assembled from short or long read data? Where did these bacte…
Comment: Am I accounting for replicates correctly in pseudobulk analysis?
by
Aspire
▴ 370
If I use Celltype_Condition as a contrast, there would be four levels : CelltypeA_Control, CelltypeA_Treated, CelltypeB_Control, CelltypeB_…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
avinci1
▴ 20
I have two bacteria genomes that I isolated and I have to know if they are the same or not, and if not, how much they are different. The pr…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
lieven.sterck
15k
what exactly do you need to compare? on the gene/protein function level or just compare absence/present of genes ? You can (crude approach…
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