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121,339 results • Page
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News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
20 minutes ago by
Claire Watson
▴ 60
0
votes
1
reply
21
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 1 hour ago by
GenoMax
151k • written 1 hour ago by
Bipin
• 0
0
votes
2
replies
31
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
43 minutes ago by
ctmfarland
• 0
2
votes
0
replies
39
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
1 hour ago by
Anton
▴ 80
2
votes
0
replies
33
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
4 hours ago by
Anton
▴ 80
2
votes
0
replies
35
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
4 hours ago by
Anton
▴ 80
838
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
2
votes
0
replies
41
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
4 hours ago by
Anton
▴ 80
0
votes
2
replies
75
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
4 hours ago by
rbpdee
▴ 50
0
votes
1
reply
69
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
updated 3 hours ago by
jared.andrews07
★ 18k • written 5 hours ago by
KABILAN
▴ 130
0
votes
7
replies
199
views
How to deal with intermediate files
procedures
data
operations
updated 2 hours ago by
GenoMax
151k • written 19 hours ago by
ramiro.barrantes
▴ 50
1
vote
1
reply
78
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 7 hours ago by
dthorbur
★ 3.0k • written 10 hours ago by
Adrian
• 0
0
votes
1
reply
69
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 6 hours ago by
GenoMax
151k • written 8 hours ago by
Luwell
• 0
0
votes
1
reply
75
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 8 hours ago by
patrickdm
▴ 260 • written 9 hours ago by
adarsh
▴ 60
1
vote
1
reply
121
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 10 hours ago by
patrickdm
▴ 260 • written 1 day ago by
andrea
• 0
0
votes
0
replies
61
views
HISAT2 or STAR
alignment
hisat2
star
12 hours ago by
Shazel
• 0
0
votes
2
replies
96
views
What to do after fastp?
rna-seq
fastp
alignment
updated 8 hours ago by
dthorbur
★ 3.0k • written 12 hours ago by
Shazel
• 0
1
vote
1
reply
241
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 1 day ago by
colindaven
7.6k • written 4 days ago by
emil.paulitz
• 0
0
votes
0
replies
85
views
ATAC-seq analysis
atac-seq
hmmratac
calling
peak
macs3
updated 1 day ago by
GenoMax
151k • written 1 day ago by
SEJAL
• 0
0
votes
1
reply
133
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 1 day ago by
GenoMax
151k • written 1 day ago by
bn
▴ 30
0
votes
0
replies
131
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 1 day ago by
GenoMax
151k • written 2 days ago by
Floren
• 0
0
votes
1
reply
468
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 2 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
138
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
2 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.0k
views
normalize between 2 different platform
RNA-Seq
updated 2 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
140
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
bioinformatics
analysis
2 days ago by
linqy
▴ 10
0
votes
1
reply
201
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 3 days ago by
GenoMax
151k • written 3 days ago by
michael.dhar
• 0
2
votes
4
replies
870
views
Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in terms of using repetitive elements to filter peaks
sequence
scatac
cell
single
10xatac
2 days ago by
gynecoloji
• 0
0
votes
2
replies
275
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
3 days ago by
Sd
• 0
0
votes
0
replies
172
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
3 days ago by
a58c4637
• 0
8
votes
5
replies
380
views
nanopore unaligned bam files
nanopore
updated 3 days ago by
GenoMax
151k • written 3 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
162
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
3 days ago by
gogeni5529
▴ 70
0
votes
1
reply
229
views
Issue with Package installation in R.
R
GCC
updated 3 days ago by
GenoMax
151k • written 3 days ago by
harsh
▴ 20
0
votes
0
replies
158
views
MAPQ algorithms of Giraffe
giraffe
vg
3 days ago by
gulin
• 0
5
votes
4
replies
635
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 3 days ago by
colindaven
7.6k • written 11 days ago by
biostars
▴ 30
0
votes
1
reply
209
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 3 days ago by
ATpoint
88k • written 3 days ago by
Vxike
• 0
2
votes
2
replies
1.8k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell
scATAC-Seq
Signac
transcriptomics
updated 3 days ago by
Jan
• 0 • written 3.6 years ago by
patelk26
▴ 340
4
votes
2
replies
276
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
3 days ago by
ATS
▴ 10
1
vote
4
replies
294
views
How to add GFP in STAR reference?
STAR
updated 3 days ago by
GenoMax
151k • written 4 days ago by
bioinfo
▴ 160
0
votes
0
replies
182
views
News:
Population Genomics Using Ancient DNA Data course
DemographicModels
PopulationGenomics
aDNA
Genomics
4 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
224
views
Can you compare GETx and TCGA miRNA non normalized counts a
comapre
to
how
updated 4 days ago by
ATpoint
88k • written 4 days ago by
radwa_noreen
• 0
0
votes
3
replies
340
views
ATAC-seq analysis
ATAC-seq
Samtools
Sorting
updated 4 days ago by
ATpoint
88k • written 5 days ago by
SEJAL
• 0
0
votes
1
reply
255
views
Learn tNGS
tNGS
updated 4 days ago by
GenoMax
151k • written 4 days ago by
hang
• 0
4
votes
3
replies
397
views
Server Requirements for long read data analysis
longreadserver
longreadanalysis
serverrequirements
Server
updated 4 days ago by
colindaven
7.6k • written 5 days ago by
genomics_student
• 0
0
votes
1
reply
258
views
The molecular signatures database (MSigDB) in R
MSigDB
updated 4 days ago by
marco.barr
▴ 170 • written 4 days ago by
Kelly
• 0
2
votes
3
replies
645
views
plotProfile Errors of DiffBind
DiffBind
4 days ago by
lijiangres
▴ 20
0
votes
0
replies
228
views
Job:
Lab Head positions at the WEHI, Melbourne Australia
LabHead
Australia
JobPosting
4 days ago by
Gordon Smyth
★ 8.1k
0
votes
0
replies
211
views
Merging single ATAC seq data sets from multiple sample
10x
4 days ago by
1769mkc
★ 1.3k
1
vote
3
replies
338
views
GSEA analysis in R
R
ranked_list
GSEA
updated 4 days ago by
ATpoint
88k • written 5 days ago by
rajdeepboral00
▴ 70
0
votes
1
reply
258
views
Assembly issues
adapters
Assembly
Spades
updated 5 days ago by
GenoMax
151k • written 5 days ago by
anna
• 0
2
votes
8
replies
550
views
Use taxdb tp get scientific names in local BLAST output
taxdb
sscinames
taxonomy
makeblastdb
blast
updated 4 days ago by
GenoMax
151k • written 6 days ago by
Luca Arbore
▴ 10
121,339 results • Page
1 of 2427
Recent Votes
How to adjust for homotypic doublets in the R package DoubletFinder
C: Remove Extra Info From Fasta Header
Remove Extra Info From Fasta Header
A: plotting a dotplot with topGO output
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
opengenes-mcp - MCP server on the database for longevity genes
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
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Recent Replies
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
ctmfarland
• 0
Thanks for the prompt response! * min: 67, max: 93,862, avg: 3,626, q25: 2737, q75: 4406 * minION * 1,150,160 reads total/used and calcula…
Comment: Error Scaffolding with RagTag
by
GenoMax
151k
Is there anything in `ragtag.scaffold.asm.paf.log` file?
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
GenoMax
151k
> the average read length in my ONT library is ~3Kbp What is the range of read lengths in this dataset? Was this run on a minION or larger…
Comment: How to deal with intermediate files
by
GenoMax
151k
Not sure I fully understand your question. Many of us use the local computer as a dumb terminal to get to the HPC where much of the work ha…
Comment: How to deal with intermediate files
by
ramiro.barrantes
▴ 50
Yes, from my laptop I do the final reports with graphs, etc and all the code is source controlled with git. I am not computing anything on …
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
jared.andrews07
★ 18k
Show example images and the code used to generate them. We can't see what you see, so it's hard to say if you are plotting things incorrect…
Comment: How to deal with intermediate files
by
GenoMax
151k
> One simpler way that is closer is for example to mount the locations on our HPC to my laptop and hence not having to transfer anything A…
Comment: How to deal with intermediate files
by
ramiro.barrantes
▴ 50
Thank you!! I am aware of all of those, however, they are not exactly what I am looking for: I could transfer data from one place to anothe…
Comment: Best pairwise alignment for insertion and deletion-containing sequences
by
rbpdee
▴ 50
Thanks, @patrickdm! Let me give it a shot.
Answer: Best pairwise alignment for insertion and deletion-containing sequences
by
patrickdm
▴ 260
Hello, I'd try tweaking the [Affine Gap Scores][1] of Align.PairwiseAligner(), and if those are not good enough, consider the possibilty to…
Comment: How to deal with intermediate files
by
dthorbur
★ 3.0k
Fair point about the sensitivity of data. I don't work on human or other particularly sensitive data so never really thought about it.
Comment: How to deal with intermediate files
by
GenoMax
151k
Great list. Globus may be the perfect option, if it is already installed on HPC. Something to consider before using any of the above. Not…
Comment: phage sequence no alignment to genome
by
GenoMax
151k
> StrainA_genome.fasta Is this a publicly available reference genome (preferably RefSeq version) for your organism (strain)? Have you comp…
Answer: How to deal with intermediate files
by
dthorbur
★ 3.0k
There are a bunch of options, and I've seen a lot of different methods over the years. Here are a few of the common ones I've seen/used: …
Answer: Quality control metrics in mmCIF
by
dthorbur
★ 3.0k
There is a lot of useful information in the mmCIF file headers that can be relevant. Each method will have slightly different information a…
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