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120,715 results • Page
1 of 2415
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0
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0
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11
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
1 hour ago by
Mark
▴ 30
2
votes
1
reply
816
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 4 hours ago by
bioinfo_enthusiast
• 0 • written 3.7 years ago by
Kumar
▴ 120
0
votes
0
replies
34
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
4 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
55
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
15 hours ago by
1769mkc
★ 1.2k
1
vote
1
reply
121
views
How to convert .ab1 to fastq
Fastq
updated 22 hours ago by
Pierre Lindenbaum
165k • written 23 hours ago by
dr.suvarnakapale
• 0
0
votes
2
replies
176
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 1 day ago by
dsull
★ 7.3k • written 1 day ago by
brutonk
• 0
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
83
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
1 day ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
156
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
updated 1 day ago by
ATpoint
87k • written 1 day ago by
ATRX
★ 1.2k
0
votes
1
reply
371
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 1 day ago by
S
• 0 • written 29 days ago by
s
• 0
0
votes
0
replies
90
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
1 day ago by
Mllepnos
• 0
2
votes
0
replies
93
views
Tool:
PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment
function
GO
goterms
geneontology
1 day ago by
geneontologyhelp
▴ 460
0
votes
0
replies
100
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
1 day ago by
Ram
45k
2
votes
1
reply
205
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
updated 1 day ago by
grover.sandeep
▴ 20 • written 3 days ago by
s.may-wilson
▴ 50
0
votes
0
replies
101
views
News:
Multi-Omics Integration with Machine Learning — Online Course!
Machine-Learning
Multi-Omics
Depp-Learning
Data-Integration
BigData
1 day ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
172
views
Alignment algorithm for DNA sequencing
sequencing
data
DNA
updated 1 day ago by
ATpoint
87k • written 1 day ago by
QX
▴ 70
0
votes
1
reply
163
views
RepeatMasker UCSC track
RepeatMasker
updated 1 day ago by
Michael
55k • written 2 days ago by
frarodmar17
• 0
0
votes
0
replies
117
views
rarefaction curve metagenomic reads show species saturation around 100 000 reads
metagenomics
rarefaction
kraken2
2 days ago by
rDNA
▴ 20
0
votes
4
replies
403
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 1 day ago by
jared.andrews07
★ 18k • written 4 days ago by
Pumla
• 0
9
votes
21
replies
7.7k
views
12 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 2 days ago by
bagdevi.mishra
▴ 110 • written 6 months ago by
Martina
• 0
0
votes
2
replies
183
views
Looking up gene name from mRNA ID using biomaRt
R
mRNA
biomaRt
updated 1 day ago by
Ram
45k • written 2 days ago by
Khôi
• 0
0
votes
0
replies
138
views
Interpreting negative gap length in MUMMER4
mummer
translocation
2 days ago by
cedric.blais
▴ 20
0
votes
0
replies
121
views
Uncertainty about deepTools computeMatrix options for RNA modifications
deepTools
metagene
computeMatrix
2 days ago by
Kyle
• 0
0
votes
0
replies
118
views
News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
2 days ago by
soledad.esteban
• 0
6
votes
6
replies
525
views
Multiple factors in DESeq2
deseq2
2 days ago by
noodlejackson
▴ 40
10
votes
2
replies
281
views
Why do RNAseq reads align to non-gene regions of the bacterial genome?
RNAseq
transcription
updated 2 days ago by
i.sudbery
21k • written 3 days ago by
Texx
▴ 40
1
vote
1
reply
246
views
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genomes
star
trinity
rnaseq
updated 2 days ago by
Ram
45k • written 2 days ago by
zizigolu
★ 4.3k
3
votes
7
replies
314
views
nanopore variant calling
pacBio
long-read
nanopore
updated 1 day ago by
colindaven
7.3k • written 2 days ago by
Meghan.T
• 0
0
votes
3
replies
284
views
enrichGo problem
enrichGo
updated 1 day ago by
Arup Ghosh
3.3k • written 2 days ago by
mimijane1664
• 0
1
vote
4
replies
282
views
Seeking Help for Reanalysis of Raw WES Data
WES
updated 2 days ago by
Jeremy Leipzig
23k • written 3 days ago by
lidia.manczak
• 0
1
vote
8
replies
289
views
Biscuit Alignment and Index failed - WGBS - Bisulfite analysis
BWA
Biscuit
Bisulfite
updated 2 days ago by
Ram
45k • written 3 days ago by
Palanikumar.Palanichamy
• 0
0
votes
3
replies
238
views
illumina: Adapter Confusion
ILLUMINA
ADAPTER
updated 2 days ago by
GenoMax
149k • written 3 days ago by
lingjun meng
▴ 20
2
votes
3
replies
258
views
Identifying primer sequences from raw FASTQ files
primers
2 days ago by
Chandini
• 0
2
votes
7
replies
1.3k
views
HTSlib threads when ingesting large bgzipped FASTA
htslib
samtools
bgzip
c
updated 2 days ago by
aw7
▴ 370 • written 20 months ago by
Oleksii
• 0
3
votes
3
replies
298
views
question for dowloading Protein fasta sequence by edirect using while
edirect
updated 3 days ago by
vkkodali_ncbi
★ 3.8k • written 4 days ago by
诗友
• 0
2
votes
2
replies
706
views
Validate RNAseq Models in Microarray Data?
microarray
rnaseq
coxlasso
fpkm
updated 2 days ago by
ATpoint
87k • written 2.7 years ago by
vitor
▴ 130
0
votes
0
replies
149
views
Restrict anlaysis of WGS VCF file to Refseq Select using snpeff
refseq
vcf
wgs
3 days ago by
Gabriel
• 0
0
votes
2
replies
253
views
Novel genes in model organisms
homologue
genome
gene
3 days ago by
zizigolu
★ 4.3k
0
votes
1
reply
241
views
Understanding sctransform
sctransform
Seurat
updated 3 days ago by
Bastien Hervé
6.1k • written 3 days ago by
Deepak Tanwar
★ 4.2k
1
vote
1
reply
259
views
Subset reads based on Phred-score ranges
phred
sequencing
ngs
updated 3 days ago by
GenoMax
149k • written 3 days ago by
Mark
▴ 30
5
votes
3
replies
333
views
Reasoning - Why is it invalid to compare ratios of TPMs?
RNAseq
analysis
expression
normalization
differential
TPM
batch
effect
updated 1 day ago by
ATpoint
87k • written 3 days ago by
VTh
• 0
2
votes
2
replies
395
views
DEGs Analysis For a Microarray Data that has one biological replicates per cell line in each condition
Analysis
DEGs
Microarray
3 days ago by
mete.han.celebi
• 0
2
votes
6
replies
420
views
The soapdenovo2 genome assembly is highly fragmented - learning genome assembly with public data
Gene
soapdenovo2
assembly
updated 3 days ago by
lieven.sterck
15k • written 4 days ago by
JieQY
• 0
0
votes
2
replies
252
views
Cytoscape COLOUR EDGES
Reulatory
Cytoscape
Networks
2 days ago by
SKY
▴ 60
3
votes
3
replies
547
views
VCF filtering with Allele Balance (AB) using FilterVcf (Picard)
Allele-Balance
FilterVcf
Picard
GATK
updated 4 days ago by
GokalpC
▴ 160 • written 16 days ago by
Eduardo
▴ 20
1
vote
4
replies
596
views
Haplotype analysis
founder
haplotype-analysis
2 days ago by
disha3786
• 0
3
votes
4
replies
382
views
Indica rice genome and annotation files
RNASeq
updated 4 days ago by
ChanderKant (CK) Chaudhary
▴ 10 • written 5 days ago by
chandimaa
• 0
2
votes
6
replies
461
views
Question: Making primers for cloning and transfection
transfection
cloning
primer
PCR
gene
updated 3 days ago by
jared.andrews07
★ 18k • written 4 days ago by
Lu Adr
• 0
0
votes
0
replies
200
views
Help with the interpretation of Silhouette width averaging
clustering
kmeans
cluster
silhouettemethod
4 days ago by
Maria Jose
• 0
0
votes
1
reply
282
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Cancer
Oncology
Tenure-earning
Faculty
Bioinformatics
updated 4 days ago by
GenoMax
149k • written 4 days ago by
maritza.garcia-saavedra
• 0
120,715 results • Page
1 of 2415
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Answer: Gene Expression Timeline Analysis for N=1
Difference between gam and sam/bam files?
Answer: How to convert .ab1 to fastq
A: AB1 to FASTQ
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Answer: How do you estimate time to complete a project or task?
Answer: How do you estimate time to complete a project or task?
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Comment: How to perform PPI network analysis in STRING for newly sequenced bacterial geno
by
bioinfo_enthusiast
• 0
Hi. How did you do it? I’m facing kind of similar situation. Thank you so much.
Answer: How to convert .ab1 to fastq
by
Pierre Lindenbaum
165k
https://www.biostars.org/p/309727/
Answer: Parsing BAM file per cell from Smart-Seq2 dataset
by
dsull
★ 7.3k
Look at the STARsolo documentation on GitHub: it shows you how to create your manifest.tsv file so that the RG flag in your BAM file conta…
Answer: Gene Expression Timeline Analysis for N=1
by
ATpoint
87k
You say time series but it's actually discrete treatments, so no time series. It is an unreplicated within patient. I would probably apply …
Comment: Parsing BAM file per cell from Smart-Seq2 dataset
by
GenoMax
149k
Based on your use of UMI's you appear to have smartseq v.3 data. Since this is single cell data I don't know if plain `STAR` is appropria…
Answer: Interactive UMAP for scRNA-seq Data
by
S
• 0
Hi, I found a great package called [ShinyCell][1] which makes interactive UMAP and many other interactive plots. It's super easy to setu…
Comment: Where Is The Experimental Rna Structure Data?
by
Wayne
★ 2.1k
Related 2025 pre-print: ['NucleoSeeker: Precision Filtering of RNA Databases to Curate High-Quality Datasets'](https://www.biorxiv.org/cont…
Comment: GERP Score for variants
by
Begonia_pavonina
▴ 210
It seems that the link http://mendel.stanford.edu/SidowLab/downloads/gerp/ is dead now. Would anyone know if it is temporary of definitive?…
Comment: Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argu
by
jared.andrews07
★ 18k
Well, the issue is what it says. You're saying your reference data is single cell, but there's only a single cell for each cell type. It ex…
Answer: How to clarify results from an HLA association analysis - Omnibus tests/HATK/oth
by
grover.sandeep
▴ 20
https://pubmed.ncbi.nlm.nih.gov/37495751/ You can reach me. Sandeep Grover
Comment: enrichGo problem
by
Arup Ghosh
3.3k
Can you share some of the gene names from the `genes` vector?
Comment: nanopore variant calling
by
colindaven
7.3k
You'll get massive coverage for just one gene (maybe 2000+ depending on how long you run the minion for), so you could consider multiple ge…
Comment: Reasoning - Why is it invalid to compare ratios of TPMs?
by
ATpoint
87k
I can only speak for myself, but I have never looked at gene ratios, nor do I see its usecase.
Comment: Alignment algorithm for DNA sequencing
by
ATpoint
87k
> some alignment of DNA sequencing This is not an adequate description of what you achieve to do. Please say why common tools, such as the…
Comment: Alignment algorithm for DNA sequencing
by
GenoMax
149k
You can use `bbmap` with the `local=t` option if you need local alignments. `bowtie v.1.x` does ungapped alignments.
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