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121,360 results • Page
1 of 2428
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0
votes
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52
views
Isoquant Major Exon Elongation
isoquant
nanopore
exon
9 hours ago by
aico
• 0
0
votes
0
replies
55
views
bcftools run-roh error
roh
bcftools
updated 9 hours ago by
GenoMax
151k • written 10 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
68
views
News:
Workshop: Virtual Single-Cell Transcriptomics, June 24–26
Transcriptomics
workshop
UConn
12 hours ago by
zsc25001
▴ 10
1
vote
6
replies
190
views
How can I find KO IDs for ORF sequences from kofam_scan ?
biology
Computational
Bioinformatics
10 hours ago by
Nikesh
• 0
0
votes
0
replies
74
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
18 hours ago by
Titus
▴ 910
0
votes
2
replies
153
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
updated 9 hours ago by
Gordon Smyth
★ 8.1k • written 20 hours ago by
rajdeepboral00
▴ 70
0
votes
0
replies
66
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
20 hours ago by
Pumla
• 0
1
vote
6
replies
209
views
Significant reads loss after fastp
fastp
loss
reads
3 hours ago by
SpliceAndScript
• 0
1
vote
1
reply
127
views
Shinyapps Server Down?
Shinyapps
Posit
updated 19 hours ago by
GenoMax
151k • written 22 hours ago by
Arup Ghosh
3.3k
0
votes
2
replies
165
views
Data of microarray
Microarray
4 hours ago by
Peter
• 0
0
votes
0
replies
99
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
21 hours ago by
Minh-Anh
▴ 10
2
votes
4
replies
246
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
13 hours ago by
aeb
▴ 20
0
votes
2
replies
184
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
23 hours ago by
SushiRoll
▴ 140
1
vote
2
replies
207
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
1 day ago by
MitchT
▴ 10
4
votes
2
replies
190
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
123
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
98
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
100
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
1 day ago by
Begonia_pavonina
▴ 210
5
votes
2
replies
202
views
required annotations for VQSR
VQSR
vcf
annotation
1 day ago by
Mahdi&Christ
▴ 20
4
votes
4
replies
304
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
480
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
180
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
654
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
457
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
139
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
319
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
159
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
142
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
154
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
161
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
197
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
406
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
177
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
174
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
175
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
220
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
208
views
HISAT2 or STAR
alignment
hisat2
star
updated 2 days ago by
rfran010
★ 1.5k • written 3 days ago by
SpliceAndScript
• 0
0
votes
2
replies
211
views
What to do after fastp?
rna-seq
fastp
alignment
updated 2 days ago by
dthorbur
★ 3.0k • written 3 days ago by
SpliceAndScript
• 0
1
vote
1
reply
334
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
184
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
224
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
217
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
557
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
224
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
229
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
298
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
369
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
Comment: FastTree error while constructing tree
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Why Does Rna-Seq Read Count Fit Poisson Distribution?
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Comment: IGV view for Chromatin accessibility ATAC-seq
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Comment: Better splitting of mutliallelic sites then bcftools norm --m-any
by
gernophil
▴ 130
Because this question just received an upvote: I used `vt decompose -s` back in the days, but I think bcftools now also makes you choose th…
Comment: Significant reads loss after fastp
by
SpliceAndScript
• 0
I have attached the phred score image of my reads, your opinion will be appreciated.
Comment: Significant reads loss after fastp
by
SpliceAndScript
• 0
I have RNA-seq data and here I am attaching the fastqc report image of ![enter image description here][1]my reads before and after running …
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 …
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