Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Post does not exist.
Limit : all time
all time
today
this week
this month
this year
121,360 results • Page
1 of 2428
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
37
views
Isoquant Major Exon Elongation
isoquant
nanopore
exon
6 hours ago by
aico
• 0
0
votes
0
replies
38
views
bcftools run-roh error
roh
bcftools
updated 5 hours ago by
GenoMax
151k • written 6 hours ago by
Pratiksha
• 0
839
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
0
votes
0
replies
55
views
News:
Workshop: Virtual Single-Cell Transcriptomics, June 24–26
Transcriptomics
workshop
UConn
9 hours ago by
zsc25001
▴ 10
1
vote
6
replies
176
views
How can I find KO IDs for ORF sequences from kofam_scan ?
biology
Computational
Bioinformatics
7 hours ago by
Nikesh
• 0
0
votes
0
replies
68
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
14 hours ago by
Titus
▴ 910
0
votes
2
replies
143
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
updated 5 hours ago by
Gordon Smyth
★ 8.1k • written 17 hours ago by
rajdeepboral00
▴ 70
0
votes
0
replies
60
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
16 hours ago by
Pumla
• 0
1
vote
4
replies
172
views
Significant reads loss after fastp
fastp
loss
reads
updated 14 hours ago by
AIMAR
▴ 10 • written 17 hours ago by
Shazel
• 0
1
vote
1
reply
122
views
Shinyapps Server Down?
Shinyapps
Posit
updated 16 hours ago by
GenoMax
151k • written 18 hours ago by
Arup Ghosh
3.3k
0
votes
2
replies
148
views
Data of microarray
Microarray
1 hour ago by
Peter
• 0
0
votes
0
replies
94
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
17 hours ago by
Minh-Anh
▴ 10
2
votes
4
replies
236
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
10 hours ago by
aeb
▴ 20
0
votes
2
replies
177
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
20 hours ago by
SushiRoll
▴ 140
1
vote
2
replies
202
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
1 day ago by
MitchT
▴ 10
3
votes
2
replies
184
views
Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
picard
updated 1 day ago by
Michael
55k • written 1 day ago by
adixon3
• 0
0
votes
0
replies
118
views
Reporting Imputed SNPs in GWAS
impute
GWAS
updated 1 day ago by
Ram
45k • written 1 day ago by
Aastha
• 0
0
votes
0
replies
93
views
Does Beagle use the reference genome for both phasing AND imputing genotypes?
beagle
genotypes
phasing
imputation
1 day ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
95
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
1 day ago by
Begonia_pavonina
▴ 210
5
votes
2
replies
195
views
required annotations for VQSR
VQSR
vcf
annotation
1 day ago by
Mahdi&Christ
▴ 20
4
votes
4
replies
296
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
1 day ago by
ctmfarland
▴ 20
9
votes
9
replies
469
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
1 day ago by
KABILAN
▴ 130
0
votes
1
reply
173
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 1 day ago by
ATpoint
88k • written 2 days ago by
Yingying
▴ 10
0
votes
1
reply
648
views
Differential Expression tests for cell-type clusters from a single-cell RNAseq dataset with no biological replicates
cell-type
DEG
DE
single-cell
updated 2 days ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
2
votes
10
replies
449
views
Annotation Issue using miRBASE gff
NGS
miRNA
updated 1 day ago by
GenoMax
151k • written 2 days ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
134
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
2 days ago by
Claire Watson
▴ 60
1
vote
6
replies
310
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 1 day ago by
Michael
55k • written 2 days ago by
Bipin
▴ 10
4
votes
0
replies
154
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
2 days ago by
Anton
▴ 100
2
votes
0
replies
137
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
2 days ago by
Anton
▴ 100
2
votes
0
replies
137
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
2 days ago by
Anton
▴ 100
2
votes
0
replies
155
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
2 days ago by
Anton
▴ 100
0
votes
2
replies
191
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
2 days ago by
rbpdee
▴ 50
2
votes
7
replies
398
views
How to deal with intermediate files
procedures
data
operations
updated 2 days ago by
GenoMax
151k • written 3 days ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
171
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 2 days ago by
dthorbur
★ 3.0k • written 2 days ago by
Adrian
• 0
0
votes
1
reply
167
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Luwell
• 0
0
votes
1
reply
170
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 2 days ago by
patrickdm
▴ 260 • written 2 days ago by
adarsh
▴ 60
1
vote
1
reply
214
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 2 days ago by
patrickdm
▴ 260 • written 3 days ago by
andrea
• 0
1
vote
1
reply
203
views
HISAT2 or STAR
alignment
hisat2
star
updated 2 days ago by
rfran010
★ 1.5k • written 2 days ago by
Shazel
• 0
0
votes
2
replies
206
views
What to do after fastp?
rna-seq
fastp
alignment
updated 2 days ago by
dthorbur
★ 3.0k • written 2 days ago by
Shazel
• 0
1
vote
1
reply
328
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 3 days ago by
colindaven
7.6k • written 6 days ago by
emil.paulitz
• 0
0
votes
0
replies
178
views
ATAC-seq analysis
atac-seq
hmmratac
calling
peak
macs3
updated 3 days ago by
GenoMax
151k • written 3 days ago by
SEJAL
• 0
0
votes
1
reply
218
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 3 days ago by
GenoMax
151k • written 3 days ago by
bn
▴ 30
0
votes
0
replies
212
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Floren
• 0
0
votes
1
reply
552
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 4 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
218
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
4 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.1k
views
normalize between 2 different platform
RNA-Seq
updated 5 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
224
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
updated 1 day ago by
Ram
45k • written 5 days ago by
linqy
▴ 10
0
votes
1
reply
293
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 5 days ago by
GenoMax
151k • written 5 days ago by
michael.dhar
• 0
2
votes
4
replies
1.3k
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
5 days ago by
gynecoloji
• 0
0
votes
2
replies
364
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
5 days ago by
Sd
• 0
121,360 results • Page
1 of 2428
Recent Votes
Why Does Rna-Seq Read Count Fit Poisson Distribution?
WGCNA- Large number of genes clustering under one Module
Comment: IGV view for Chromatin accessibility ATAC-seq
Answer: Shinyapps Server Down?
Answer: How can I find KO IDs for ORF sequences from kofam_scan ?
Comment: Significant reads loss after fastp
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
Recent Locations •
All
United States,
just now
Australia,
1 minute ago
India,
9 minutes ago
United States,
12 minutes ago
Australia,
28 minutes ago
India,
39 minutes ago
United States,
46 minutes ago
Recent Awards •
All
Popular Question
to
Chirag Parsania
★ 2.0k
Teacher
to
Ram
45k
Popular Question
to
Leite
★ 1.3k
Popular Question
to
marongiu.luigi
▴ 740
Popular Question
to
marco.barr
▴ 170
Commentator
to
GenoMax
151k
Popular Question
to
mohammadhassanj
▴ 260
Recent Replies
Comment: Data of microarray
by
Peter
• 0
sorry but I do not have input file. If you have can you offer to me?
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
• 0
Thank you, I changed it as #SBATCH --time=1-00:00:00 and it's running. I will keep you updated and thanks again.
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
aeb
▴ 20
Thanks for your input. I read STAR is generally not meant to align to the transcriptome and there would be other more optimized ways to do …
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
aeb
▴ 20
Thanks for your response! I understand the cost difference may not be much... I am considering to compare this approach to just aligning to…
Answer: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Mensur Dlakic
★ 29k
Already answered in your other post. I suggest you inquire about the SLURM time limit and set it to a maximum value allowed. This would …
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Mensur Dlakic
★ 29k
What @genomax said. I suggest you inquire about the SLURM time limit and set it to a maximum value allowed. This would be 6 days: #SBA…
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
• 0
This is one of sequence; >k127_52915239_12 # 4220 # 5476 # -1 # ID=1511550_12;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=11bp;gc_…
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
GenoMax
151k
Looking at the command line you used and the manual for kofam_scan, multi-threading should be in use. How long are your query sequences? …
Comment: How can I find KO IDs for ORF sequences from kofam_scan ?
by
Nikesh
• 0
The same error is occurring. I’m wondering if parallel processing is not being utilized during the execution.
Answer: How can I find KO IDs for ORF sequences from kofam_scan ?
by
GenoMax
151k
Please don't post the same content in multiple places. > I tried changing differenet cpu allocation too. As I wrote in the other comment…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
GenoMax
151k
> JOB 10654468 ON c2023 CANCELLED AT 2025-06-10T21:46:45 DUE TO TIME LIMIT *” You are asking for one minute less than 6 hours in your SLUR…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Nikesh
• 0
@mensur Hi, I set up the environment in HCC, and my FASTA file contains 98 sequences. This is my SLURM script, but I’ve tried running it …
Comment: Significant reads loss after fastp
by
AIMAR
▴ 10
Hi, concerning your read size in your command you've specified to keep reads with a minimum length of 50 bp with the option `--length_requi…
Answer: Isoform analysis after quantification with Salmon/Star
by
Gordon Smyth
★ 8.1k
The following papers show the advantages of Salmon with Gibbs resampling, followed by edgeR's catchSalmon, glmQLFit, glmQLFTest (for DTE) a…
Comment: Significant reads loss after fastp
by
GenoMax
151k
What kind of data is this? Changing default parameters for programs should be done based on an understanding of the characteristics of your…
Traffic: 2765 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6