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121,356 results • Page
1 of 2428
Sort: Rank
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Votes
Replies
0
votes
0
replies
13
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
57 minutes ago by
Titus
▴ 910
0
votes
2
replies
70
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
updated 1 hour ago by
Gordon Smyth
★ 8.1k • written 3 hours ago by
rajdeepboral00
▴ 70
0
votes
0
replies
23
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
2 hours ago by
Pumla
• 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
4
replies
78
views
Significant reads loss after fastp
fastp
loss
reads
updated 21 minutes ago by
AIMAR
▴ 10 • written 3 hours ago by
Shazel
• 0
0
votes
1
reply
66
views
Shinyapps Server Down?
Shinyapps
Posit
updated 2 hours ago by
GenoMax
151k • written 4 hours ago by
Arup Ghosh
3.3k
0
votes
1
reply
84
views
Data of microarray
Microarray
updated 2 hours ago by
1769mkc
★ 1.3k • written 9 hours ago by
Peter
• 0
0
votes
0
replies
71
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
3 hours ago by
Minh-Anh
▴ 10
2
votes
2
replies
156
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
updated 15 hours ago by
dsull
★ 7.6k • written 19 hours ago by
aeb
▴ 20
0
votes
2
replies
143
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
6 hours ago by
SushiRoll
▴ 140
1
vote
2
replies
175
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
18 hours ago by
MitchT
▴ 10
3
votes
2
replies
159
views
Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
picard
updated 20 hours ago by
Michael
55k • written 23 hours ago by
adixon3
• 0
0
votes
0
replies
98
views
Reporting Imputed SNPs in GWAS
impute
GWAS
updated 19 hours ago by
Ram
45k • written 1 day ago by
Aastha
• 0
0
votes
0
replies
74
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
75
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
1 day ago by
Begonia_pavonina
▴ 210
5
votes
2
replies
171
views
required annotations for VQSR
VQSR
vcf
annotation
22 hours ago by
Mahdi&Christ
▴ 20
3
votes
4
replies
266
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
19 hours ago by
ctmfarland
▴ 20
9
votes
9
replies
432
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
23 hours ago by
KABILAN
▴ 130
0
votes
1
reply
151
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 1 day ago by
ATpoint
88k • written 1 day ago by
Yingying
▴ 10
0
votes
1
reply
629
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 1 day ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
2
votes
10
replies
409
views
Annotation Issue using miRBASE gff
NGS
miRNA
updated 13 hours ago by
GenoMax
151k • written 1 day ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
116
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
1 day ago by
Claire Watson
▴ 60
1
vote
6
replies
286
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 18 hours ago by
Michael
55k • written 1 day ago by
Bipin
▴ 10
3
votes
0
replies
131
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
1 day ago by
Anton
▴ 90
2
votes
0
replies
119
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
1 day ago by
Anton
▴ 90
2
votes
0
replies
117
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
1 day ago by
Anton
▴ 90
2
votes
0
replies
134
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
1 day ago by
Anton
▴ 90
0
votes
2
replies
172
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
370
views
How to deal with intermediate files
procedures
data
operations
updated 1 day ago by
GenoMax
151k • written 2 days ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
155
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
150
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
152
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
197
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 2 days ago by
patrickdm
▴ 260 • written 2 days ago by
andrea
• 0
1
vote
1
reply
185
views
HISAT2 or STAR
alignment
hisat2
star
updated 1 day ago by
rfran010
★ 1.5k • written 2 days ago by
Shazel
• 0
0
votes
2
replies
186
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
311
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 2 days ago by
colindaven
7.6k • written 5 days ago by
emil.paulitz
• 0
0
votes
0
replies
157
views
ATAC-seq analysis
atac-seq
hmmratac
calling
peak
macs3
updated 2 days ago by
GenoMax
151k • written 2 days ago by
SEJAL
• 0
0
votes
1
reply
202
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
195
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 3 days ago by
GenoMax
151k • written 4 days ago by
Floren
• 0
0
votes
1
reply
532
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
201
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 4 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
204
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
updated 19 hours ago by
Ram
45k • written 4 days ago by
linqy
▴ 10
0
votes
1
reply
275
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 4 days ago by
GenoMax
151k • written 4 days ago by
michael.dhar
• 0
2
votes
4
replies
1.2k
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
4 days ago by
gynecoloji
• 0
0
votes
2
replies
348
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
5 days ago by
Sd
• 0
0
votes
0
replies
235
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
5 days ago by
a58c4637
• 0
8
votes
5
replies
500
views
nanopore unaligned bam files
nanopore
updated 5 days ago by
GenoMax
151k • written 5 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
250
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
5 days ago by
gogeni5529
▴ 70
0
votes
1
reply
299
views
Issue with Package installation in R.
R
GCC
updated 4 days ago by
GenoMax
151k • written 5 days ago by
harsh
▴ 20
121,356 results • Page
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Comment: Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
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normalization for unsupervised analysis by DESeq2
Answer: normalization for unsupervised analysis by DESeq2
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Answer: What is the difference between norm --multiallelics -any versus --atomize?
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Recent Replies
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
These papers show the advantages of Salmon with Gibbs resampling, followed by edgeR's catchSalmon, glmQLFit and diffSplice: Baldoni PL#, C…
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…
Comment: Significant reads loss after fastp
by
Shazel
• 0
Thanks for the reply. The experiment cannot be run again so I need to proceed with this data. It would be helpful if you could give me an i…
Answer: Shinyapps Server Down?
by
GenoMax
151k
https://downforeveryoneorjustme.com/ Site may have recovered since you posted the original message but https://www.shinyapps.io/ is up now.
Comment: Data of microarray
by
1769mkc
★ 1.3k
question not clear are you asking for input files or you have input file which is not working ?
Comment: Significant reads loss after fastp
by
GenoMax
151k
> I observed that phred score was not very good in my data and especially phred score of R2 was terrible, so I did fastp If the data is b…
Answer: Isoform analysis after quantification with Salmon/Star
by
i.sudbery
21k
It depends on what level you would like your analysis to take place on. In general, if you are interested in complete isoforms, then Salmon…
Comment: Time scaled tree with IQTree giving off looking branch length
by
SushiRoll
▴ 140
Hey cfos! Thanks for the reply! I did apply the ascertainment correction model, in fact I applied GTR+F+ASC for this tree. I'm wondering if…
Comment: Annotation Issue using miRBASE gff
by
GenoMax
151k
That is probably fine since you are counting only the miRNA using that GTF. You already compressed the data by desuplicating UMI. Take a lo…
Comment: Annotation Issue using miRBASE gff
by
anthony.santana.703.j
▴ 30
Hello Geno, I figured out part of my issue, my gtf file was corrupt, and I also changed my featureCounts params: featureCounts -F GTF…
Answer: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
dsull
★ 7.6k
Honestly, I'd just stick with `STAR` for this purpose. You can use the `--outReadsUnmapped` option to directly output the unmapped reads in…
Answer: Time scaled tree with IQTree giving off looking branch length
by
cfos4698
★ 1.1k
Did you remove invariant (constant) sites from the SNP alignment? If so, you should probably also be specifying an ascertainment bias corre…
Answer: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
by
GenoMax
151k
> my guess is this would be cheaper/faster than just aligning all of them to the genome to begin with If you are paying for all of your co…
Comment: Annotation Issue using miRBASE gff
by
anthony.santana.703.j
▴ 30
Thank you but, didnt make a difference, let me see what I can find, there has to be a reason.
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