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120,478 results • Page
1 of 2410
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Votes
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0
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0
replies
8
views
An alternative to haplotype phasing - assembly?
samtools
assembly
BAM
spades
phasing
1 hour ago by
Jess
▴ 40
0
votes
0
replies
14
views
How to remove rows with empty gene symbols from a seurat object?
seurat
39 minutes ago by
Chris
▴ 360
828
votes
169
replies
167k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
2
votes
3
replies
39
views
Affine versus Linear Alignment
linear-alignment
affine-score
updated 1 hour ago by
Ram
44k • written 2 hours ago by
per
• 0
0
votes
0
replies
19
views
how to make/get the SNP annotation file for running TORUS
TORUS
Annotation
SNP
GWAS
updated 2 hours ago by
GenoMax
149k • written 2 hours ago by
lee
• 0
0
votes
1
reply
28
views
Flongle 16srRNA nanopore sequencing
R.9.4.1
flow
flongle
updated 1 hour ago by
GenoMax
149k • written 2 hours ago by
Major ginger
• 0
0
votes
2
replies
99
views
Genomes with existing T2T assemblies?
T2T
genome
assembly
reference
updated 3 hours ago by
cmdcolin
★ 4.1k • written 6 hours ago by
predeus
★ 2.1k
0
votes
1
reply
72
views
R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Plasmablasts – Contradicts Biological Knowledge
CytoTRACE2
updated 53 minutes ago by
yura.grabovska
▴ 690 • written 3 hours ago by
Binghong
▴ 20
1
vote
2
replies
79
views
Installing ggpubr in Docker container rocker/r-base??
ggpubr
dockerfile
docker
r
updated 2 hours ago by
Ram
44k • written 5 hours ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
35
views
News:
Bayesian Data Analysis in R course - online, March 3-7
Bayesian
Statistics
R
6 hours ago by
Physalia-courses
★ 2.6k
3
votes
5
replies
127
views
Should we cite sed / awk in papers?
sed
awk
updated 2 hours ago by
ATpoint
87k • written 6 hours ago by
amy__
▴ 250
0
votes
0
replies
32
views
Briggs model parametes
Briggs
damage
Gargammel
6 hours ago by
anna.utili
• 0
3
votes
6
replies
183
views
Nanopore sequencing - plasmid assembly length confusion
assembly
long
nanopore
reads
updated 3 hours ago by
GenoMax
149k • written 8 hours ago by
abedkurdi10
▴ 190
0
votes
0
replies
49
views
Post-GWAS colocalization analysis VS. variant annotation, what's the difference?
variant
annotation
snp
colocalization
GWAS
8 hours ago by
sarfdezco
• 0
0
votes
0
replies
55
views
EDTA ,Transposon detection, repeat modeler and masker
homology_based_TE_detection
fragmentedTE
11 hours ago by
manaswiniparija3
▴ 50
2
votes
8
replies
472
views
Finding ORFs in a FASTA file
MatrixScore
ORFs
Motifs
MotifScoring
updated 8 hours ago by
Michael
55k • written 4 days ago by
Melissa
• 0
2
votes
3
replies
179
views
Ilumina Low quality bases at first 20 cycles + PHIX problem
Sequencing
updated 8 hours ago by
GenoMax
149k • written 1 day ago by
alenew.am
▴ 10
0
votes
3
replies
142
views
HMP dataset download issue (403 error)
HMP
dataset
microbiome
updated 12 hours ago by
GenoMax
149k • written 18 hours ago by
Emily
▴ 70
0
votes
1
reply
89
views
Enrichment Analysis for cCREs
Enrichment
statstest
bedtools
cCREs
fishers
updated 9 hours ago by
ATpoint
87k • written 20 hours ago by
alexanderturco1
• 0
0
votes
0
replies
76
views
Job:
Postdoctoral Research Position: Developing Novel Algorithms and Tools for Circular RNA Analysis
circRNAs
biology
bioinformatics
computational
21 hours ago by
Tobias Jakobi
• 0
6
votes
10
replies
622
views
Per Sequence GC Content fail
fastqc
3 hours ago by
Eduardo
• 0
0
votes
10
replies
315
views
6 follow
Phylogenetic tree from whole genome using BUSCO
BUSCO
whole_genome
phylogenetic_tree
updated 4 hours ago by
shelkmike
★ 1.5k • written 1 day ago by
manaswiniparija3
▴ 50
0
votes
0
replies
77
views
Repetitive sequences analysis
Repetitive
sequences
1 day ago by
frarodmar17
• 0
8
votes
7
replies
6.4k
views
has anyone use trimmomatic with NEBNext adaptors
rna-seq
updated 1 day ago by
Johan Zicola
▴ 80 • written 6.3 years ago by
eozcan
▴ 10
2
votes
1
reply
110
views
t2t RNAseq alignment with STAR
chm13
t2t
RNAseq
updated 16 hours ago by
GenoMax
149k • written 1 day ago by
eva_u
▴ 30
2
votes
0
replies
118
views
Herald:
The Biostar Herald for Wednesday, February 19, 2025
herald
1 day ago by
Biostar
3.4k
1
vote
2
replies
143
views
Cell Type annotation showing Normal cells as Cancer cells in single cell analysis.
seurat
Single_cell
spatial-transcriptomics
updated 1 day ago by
GenoMax
149k • written 1 day ago by
geno89
▴ 10
0
votes
0
replies
74
views
Running NGSadmix with pre-calculated ancestral genotype freqs?
admixture
ngsadmix
lcwgs
angsd
1 day ago by
j.smout.1
• 0
5
votes
5
replies
349
views
Differential Expression and absolute expression
normal
DEG
tumour
rna
1 day ago by
jain72744
▴ 10
0
votes
3
replies
246
views
Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
assembly
Metagenomic
updated 15 hours ago by
GenoMax
149k • written 1 day ago by
chemokine-1
▴ 10
0
votes
1
reply
122
views
Differetial analysis EdgeR
Differetial
EdgeR
analysis
updated 1 day ago by
ATpoint
87k • written 1 day ago by
maryak
▴ 20
0
votes
3
replies
152
views
Can I compare Gene Expression in T Cells from PBMCs vs. Tumor Tissue (for match samples)?
batch-effect-correction
integration
scRNAseq
single-cell
harmony
updated 1 day ago by
ATpoint
87k • written 1 day ago by
Saeedeh Salehi
▴ 10
1
vote
0
replies
113
views
Rules for Assigning Start and End Phase to Coding Exons
stare_phase
reading_frame
end_phase
1 day ago by
Milica
▴ 10
0
votes
2
replies
149
views
multiBamSummary
deepTools
multiBamSummary
reverse-strand
updated 1 day ago by
Ram
44k • written 1 day ago by
Hina
• 0
1
vote
2
replies
192
views
How to convert CIGAR string to VCF?
CIGAR
VCF
alignment
variant-calling
updated 1 day ago by
Ram
44k • written 2 days ago by
Biomonika (Noolean)
3.2k
0
votes
0
replies
109
views
Pooles sequencing as Somativ-Germline SNV analysis
Variant-calling
Pooled-Sequencing
Varscan
updated 1 day ago by
Ram
44k • written 2 days ago by
Milly
• 0
0
votes
0
replies
141
views
Haplotype analysis
founder
haplotype-analysis
updated 1 day ago by
Ram
44k • written 2 days ago by
disha3786
• 0
5
votes
5
replies
272
views
Extract FUngal mRNA from RNAseq Data
rnaseq
rna
fungus
humant2t
transcriptomics
updated 2 days ago by
GenoMax
149k • written 2 days ago by
SomeOne
▴ 170
0
votes
1
reply
131
views
PyMOL truncates part of structure when exporting as .pdb
pymol
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
jdoesstuff
• 0
0
votes
0
replies
430
views
Job:
Research Technician (Bioinformatics Analyst) - Computational Biology Core, Institute for Systems Genomics, UConn
Bioinformatics-Analyst
Research-Technician
2 days ago by
spu24005
• 0
0
votes
1
reply
201
views
CLI Downloading from Human Microbiome Project Given Login + contact failure
Microbiome
HMP
updated 2 days ago by
Arup Ghosh
3.3k • written 2 days ago by
Maxwell
▴ 50
1
vote
2
replies
253
views
How to predict targets of miRNAs with indels in the seed region?
seed
indels
targets
miRNA
updated 3 days ago by
ATpoint
87k • written 3 days ago by
jhonatan.henrique
• 0
0
votes
2
replies
1.3k
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)
transcriptomics
scRNAseq
singleCell
3 days ago by
ecSeq Bioinformatics
▴ 10
7
votes
3
replies
336
views
How to determine new bacterial species from custom isolate?
species
genome
submission
updated 3 days ago by
michael.ante
★ 4.0k • written 4 days ago by
marongiu.luigi
▴ 740
3
votes
1
reply
211
views
Plink removing a lot of samples
PLINK2
plink
GWAS
updated 1 day ago by
GenoMax
149k • written 3 days ago by
Steven
▴ 30
3
votes
6
replies
3.6k
views
How To Retrieve The Rna Type From A Pdb File?
rna
pdb
updated 3 days ago by
Eugene F. Baulin
▴ 20 • written 12.9 years ago by
Noam N. Kremen
▴ 60
2
votes
1
reply
195
views
How to Analyze 10x Genomics Data with Full-Length R1 and R2 (100bp Each)?
10x-Genomics
UMI
single-cell
RNA-Seq
CellRanger
updated 3 days ago by
GenoMax
149k • written 3 days ago by
zbidav
▴ 30
0
votes
0
replies
138
views
Mapping OMIM IDs (for diseases) to MeSH IDs
phenotype
ontology
DISEASE
MESH
OMIM
3 days ago by
singhankit973
• 0
1
vote
3
replies
1.1k
views
Gini Coefficient and Lorenz curve to measure uniformity of coverage
gini
lorenz curve
coverage uniformity
updated 2 days ago by
abascalfederico
★ 1.2k • written 5.0 years ago by
am
▴ 70
2
votes
6
replies
358
views
DESeq2 for multiple groups
usegalaxy
Limma
voom
Deseq2
3 days ago by
banaalkhayrat123
• 0
120,478 results • Page
1 of 2410
Recent Votes
Answer: Affine versus Linear Alignment
Comment: Affine versus Linear Alignment
Answer: Installing ggpubr in Docker container rocker/r-base??
Answer: Filter SAM file for read pairs that align on same strand
Answer: Cytoscape Or Gephi?
Answer: Cytoscape Or Gephi?
The Biostar Herald for Wednesday, February 19, 2025
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Recent Replies
Comment: R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Pla
by
yura.grabovska
▴ 690
I think expression-based estimations like "potency score" and the broader concept of trajectories are prone to being affected by the rate o…
Comment: Affine versus Linear Alignment
by
Ram
44k
I was wrong - I eyeballed it and missed a few gap openings - you are correct, there are 5 openings. So the total is 5 opens (-50) + 3 ext (…
Comment: Affine versus Linear Alignment
by
per
• 0
Could you correct my understanding, I see 5 gap openings? I placed stars above the openings ``` * * * * * T A T G T -…
Comment: Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
by
Basti
★ 2.0k
At least two samples in one group
Comment: Installing ggpubr in Docker container rocker/r-base??
by
Ram
44k
Adding to this point, the multiple `install.packages` layers have not only no advantage, but a HUEGE disadvantage: Each RUN adds a layer th…
Comment: Flongle 16srRNA nanopore sequencing
by
GenoMax
149k
Please contact ONT tech support and/or your local nanopore field applications scientist. They would likely be able to take a look at your d…
Answer: Affine versus Linear Alignment
by
Ram
44k
EDIT: I was wrong, please see comments below. Once a gap is opened, only the gap extension score (the `-1`) applies. With affine penalty, …
Comment: ERROR: SAM file generated by BWA is corrupted and cannot be processed with SAMTO
by
jkbonfield
★ 1.3k
It's probably a result of using nohup, or I think some batch schedulers may do this internally and suffer from similar issues of mixing std…
Comment: Should we cite sed / awk in papers?
by
ATpoint
87k
That having said, documenting exact software versions, at best via some sort of container, less accurate being a conda environment, even le…
Comment: Should we cite sed / awk in papers?
by
jkbonfield
★ 1.3k
Generally I've never bothered citing computer languages or fundamental tools like that. If it comes preinstalled with the OS, that's a pre…
Comment: Nanopore sequencing - plasmid assembly length confusion
by
GenoMax
149k
Was the plasmid isolated before library prep? How was the lib prep done?
Comment: Per Sequence GC Content fail
by
Eduardo
• 0
Thanks for showing me another way to see coverage. I am going to try this too. I did a Nexflow pipeline (Sarek) and obtained a better resul…
Comment: Per Sequence GC Content fail
by
Eduardo
• 0
Thanks, I did an germline pipeline with nextflow Sarek.
Answer: Genomes with existing T2T assemblies?
by
cmdcolin
★ 4.1k
this is perhaps one angle which is to search NCBI Genomes for "Complete" genome assemblies. The levels of completeness are contig->scaffold…
Comment: Phylogenetic tree from whole genome using BUSCO
by
shelkmike
★ 1.5k
Why do you think that being "much more diverged from each other than expected" is a problem?<br> Also, are you sure that you took sequences…
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