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121,349 results • Page
1 of 2427
Sort: Rank
Rank
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Votes
Replies
2
votes
2
replies
84
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
updated 10 minutes ago by
dsull
★ 7.6k • written 4 hours ago by
aeb
▴ 20
0
votes
1
reply
65
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
updated 53 minutes ago by
cfos4698
★ 1.1k • written 12 hours ago by
SushiRoll
▴ 140
1
vote
2
replies
117
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
3 hours ago by
MitchT
▴ 10
2
votes
2
replies
108
views
Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
picard
updated 5 hours ago by
Michael
55k • written 8 hours ago by
adixon3
• 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
73
views
Reporting Imputed SNPs in GWAS
impute
GWAS
updated 4 hours ago by
Ram
45k • written 10 hours ago by
Aastha
• 0
0
votes
0
replies
50
views
Does Beagle use the reference genome for both phasing AND imputing genotypes?
beagle
genotypes
phasing
imputation
11 hours ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
50
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
11 hours ago by
Begonia_pavonina
▴ 210
5
votes
2
replies
132
views
required annotations for VQSR
VQSR
vcf
annotation
7 hours ago by
Mahdi&Christ
▴ 20
1
vote
4
replies
218
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
4 hours ago by
ctmfarland
▴ 10
9
votes
9
replies
372
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
8 hours ago by
KABILAN
▴ 130
0
votes
1
reply
120
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 15 hours ago by
ATpoint
88k • written 23 hours ago by
Yingying
▴ 10
0
votes
1
reply
603
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 23 hours ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
2
votes
8
replies
281
views
Annotation Issue using miRBASE gff
NGS
miRNA
2 hours ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
90
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
234
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 3 hours ago by
Michael
55k • written 1 day ago by
Bipin
▴ 10
3
votes
0
replies
104
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
92
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
92
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
108
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
144
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
1 day ago by
rbpdee
▴ 50
1
vote
7
replies
318
views
How to deal with intermediate files
procedures
data
operations
updated 1 day ago by
GenoMax
151k • written 1 day ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
129
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
Adrian
• 0
0
votes
1
reply
124
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Luwell
• 0
0
votes
1
reply
124
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 1 day ago by
patrickdm
▴ 260 • written 1 day ago by
adarsh
▴ 60
1
vote
1
reply
174
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 1 day ago by
patrickdm
▴ 260 • written 2 days ago by
andrea
• 0
1
vote
1
reply
155
views
HISAT2 or STAR
alignment
hisat2
star
updated 1 day ago by
rfran010
★ 1.5k • written 1 day ago by
Shazel
• 0
0
votes
2
replies
153
views
What to do after fastp?
rna-seq
fastp
alignment
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
Shazel
• 0
1
vote
1
reply
289
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
132
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
179
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 2 days ago by
GenoMax
151k • written 2 days ago by
bn
▴ 30
0
votes
0
replies
174
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 3 days ago by
GenoMax
151k • written 3 days ago by
Floren
• 0
0
votes
1
reply
509
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 3 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
179
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
3 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.1k
views
normalize between 2 different platform
RNA-Seq
updated 3 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
183
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
updated 4 hours ago by
Ram
45k • written 3 days ago by
linqy
▴ 10
0
votes
1
reply
249
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
1.1k
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
325
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
4 days ago by
Sd
• 0
0
votes
0
replies
211
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
4 days ago by
a58c4637
• 0
8
votes
5
replies
465
views
nanopore unaligned bam files
nanopore
updated 4 days ago by
GenoMax
151k • written 4 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
220
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
4 days ago by
gogeni5529
▴ 70
0
votes
1
reply
275
views
Issue with Package installation in R.
R
GCC
updated 4 days ago by
GenoMax
151k • written 4 days ago by
harsh
▴ 20
0
votes
0
replies
204
views
MAPQ algorithms of Giraffe
giraffe
vg
4 days ago by
gulin
• 0
5
votes
4
replies
686
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 4 days ago by
colindaven
7.6k • written 13 days ago by
biostars
▴ 30
0
votes
1
reply
251
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 4 days ago by
ATpoint
88k • written 4 days ago by
Vxike
• 0
2
votes
2
replies
1.9k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell
scATAC-Seq
Signac
transcriptomics
updated 5 days ago by
Jan
• 0 • written 3.6 years ago by
patelk26
▴ 340
4
votes
2
replies
325
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
4 days ago by
ATS
▴ 10
1
vote
4
replies
344
views
How to add GFP in STAR reference?
STAR
updated 5 days ago by
GenoMax
151k • written 5 days ago by
bioinfo
▴ 160
0
votes
0
replies
224
views
News:
Population Genomics Using Ancient DNA Data course
DemographicModels
PopulationGenomics
aDNA
Genomics
5 days ago by
Physalia-courses
★ 2.6k
121,349 results • Page
1 of 2427
Recent Votes
Answer: Heatmap for visualizing the differentially expressed genes in RNA-seq data
Comment: Annotation Issue using miRBASE gff
Signature Matrix Modifications/Subclustering
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
struggling in using bcftools to set variants to missing
Identify transgene insert loci/copy number in nanopore De-novo assembly
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
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Recent Replies
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.
Comment: Signature Matrix Modifications/Subclustering
by
MitchT
▴ 10
Thank you. Sorry, I should have prefaced that I was able to find canonical markers of these cells in my main cluster, which is a mixture of…
Comment: Error Scaffolding with RagTag
by
Michael
55k
>Troubleshooting Steps: Ran minimap2 manually on Pritchett’s reference (attraktion.fasta) and query (pt2_busco.fa); it generated a 442 MB .…
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
ctmfarland
▴ 10
That was an excellent idea. I used blastn to pull out all ONT reads containing some/all of the gene of interest and mapped that to the refe…
Comment: Annotation Issue using miRBASE gff
by
GenoMax
151k
Looking at the alignment file we know the reference chromosome names match the GTF from miRBase. So that should be fine. Your reads are als…
Comment: Annotation Issue using miRBASE gff
by
anthony.santana.703.j
▴ 30
samtools view: LH00150:566:22TM3VLT3:6:2196:18797:12321_CTTTTCTGCCTA 16 chr1 10571 255 16M * 0 0 …
Comment: Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
by
Michael
55k
"Wow those M-chips really are fast!" possibly this. Especially with the M4 (essentially a laptop chip) when it comes to single thread perfo…
Comment: Error Scaffolding with RagTag
by
GenoMax
151k
If the run stops at the same point in the pritchett file then you should examine that to see if there is any data corruption. Make sure the…
Comment: Error Scaffolding with RagTag
by
Bipin
▴ 10
There was nothing on SLURM logs, the error mentioned above is in the error file. For Madsen, log file looks similar but is complete. For Pr…
Comment: required annotations for VQSR
by
Mahdi&Christ
▴ 20
I truly appreciate your clear and comprehensive explanation. I learned a lot of important and practical points.
Comment: Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
by
GenoMax
151k
If you were planning to do comparisons, should you not make sure that the software versions were identical on both platforms. OpenJDK as w…
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
KABILAN
▴ 130
Thank you for your comment. Now, I will go for interpretation
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