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120,452 results • Page
1 of 2410
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Votes
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0
votes
0
replies
44
views
Rules for Assigning Start and End Phase to Coding Exons
stare_phase
reading_frame
end_phase
5 hours ago by
Milica
• 0
0
votes
2
replies
72
views
multiBamSummary
deepTools
multiBamSummary
reverse-strand
updated 6 hours ago by
Ram
44k • written 6 hours ago by
Hina
• 0
828
votes
169
replies
167k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
1
reply
70
views
Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
assembly
Metagenomic
updated 6 hours ago by
Mensur Dlakic
★ 29k • written 7 hours ago by
chemokine-1
▴ 10
0
votes
2
replies
105
views
How to convert CIGAR string to VCF?
CIGAR
VCF
alignment
variant-calling
updated 6 hours ago by
Ram
44k • written 11 hours ago by
Biomonika (Noolean)
3.2k
0
votes
0
replies
47
views
Pooles sequencing as Somativ-Germline SNV analysis
Variant-calling
Pooled-Sequencing
Varscan
updated 6 hours ago by
Ram
44k • written 12 hours ago by
Milly
• 0
0
votes
0
replies
74
views
Haplotype analysis
founder
haplotype-analysis
updated 6 hours ago by
Ram
44k • written 16 hours ago by
disha3786
• 0
3
votes
5
replies
177
views
Extract FUngal mRNA from RNAseq Data
rnaseq
rna
fungus
humant2t
transcriptomics
updated 2 hours ago by
GenoMax
149k • written 18 hours ago by
SomeOne
▴ 170
3
votes
2
replies
156
views
Differential Expression and absolute expression
normal
DEG
tumour
rna
updated 18 hours ago by
andres.firrincieli
3.8k • written 20 hours ago by
jain72744
▴ 10
0
votes
1
reply
70
views
PyMOL truncates part of structure when exporting as .pdb
pymol
updated 23 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
jdoesstuff
• 0
0
votes
0
replies
163
views
Job:
Research Technician (Bioinformatics Analyst) - Computational Biology Core, Institute for Systems Genomics, UConn
Bioinformatics-Analyst
Research-Technician
8 hours ago by
spu24005
• 0
0
votes
1
reply
126
views
CLI Downloading from Human Microbiome Project Given Login + contact failure
Microbiome
HMP
updated 13 hours ago by
Arup Ghosh
3.3k • written 1 day ago by
Maxwell
▴ 50
1
vote
2
replies
189
views
How to predict targets of miRNAs with indels in the seed region?
seed
indels
targets
miRNA
updated 1 day ago by
ATpoint
87k • written 2 days ago by
jhonatan.henrique
• 0
0
votes
2
replies
1.2k
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)
transcriptomics
scRNAseq
singleCell
1 day ago by
ecSeq Bioinformatics
▴ 10
7
votes
3
replies
266
views
How to determine new bacterial species from custom isolate?
species
genome
submission
updated 1 day ago by
michael.ante
★ 4.0k • written 2 days ago by
marongiu.luigi
▴ 740
3
votes
1
reply
148
views
Plink removing a lot of samples
PLINK2
plink
GWAS
updated 19 hours ago by
chrchang523
11k • written 1 day ago by
Steven
▴ 30
3
votes
6
replies
3.6k
views
How To Retrieve The Rna Type From A Pdb File?
rna
pdb
updated 1 day ago by
Eugene F. Baulin
▴ 20 • written 12.9 years ago by
Noam N. Kremen
▴ 60
1
vote
1
reply
130
views
How to Analyze 10x Genomics Data with Full-Length R1 and R2 (100bp Each)?
10x-Genomics
UMI
single-cell
RNA-Seq
CellRanger
updated 1 day ago by
GenoMax
149k • written 1 day ago by
zbidav
▴ 30
0
votes
0
replies
83
views
Mapping OMIM IDs (for diseases) to MeSH IDs
phenotype
ontology
DISEASE
MESH
OMIM
1 day ago by
singhankit973
• 0
1
vote
3
replies
1.1k
views
Gini Coefficient and Lorenz curve to measure uniformity of coverage
gini
lorenz curve
coverage uniformity
updated 16 hours ago by
abascalfederico
★ 1.2k • written 5.0 years ago by
am
▴ 70
2
votes
6
replies
269
views
DESeq2 for multiple groups
usegalaxy
Limma
voom
Deseq2
1 day ago by
banaalkhayrat123
• 0
1
vote
2
replies
356
views
Bowtie index size / richness matters ?
bowtie
1 day ago by
maschi88
• 0
0
votes
0
replies
95
views
juicer_tools for analyzing Hi-C data
juicer_tools
7 hours ago by
Bioinformatics_16
• 0
0
votes
1
reply
149
views
Limma Voom
Differential
analysis
updated 1 day ago by
ATpoint
87k • written 1 day ago by
maryak
▴ 20
0
votes
0
replies
79
views
Blog:
Novogene Single-cell and Spatial Multi-omics Case Study: Application in Bone Regeneration
Multi-omics
Single-cell
1 day ago by
Novogene
▴ 460
0
votes
1
reply
130
views
SNP density visualization with circos in galaxy
visualization
CIRCOS
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
ag18090
• 0
0
votes
2
replies
178
views
Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing
scMultiome
10x
fastq
human-cell-atlas
cellranger-arc
4 hours ago by
Wu-Sheng Zhang
• 0
0
votes
2
replies
234
views
Merge Seurat objects
seurat
merge
single-cell
updated 1 day ago by
Ram
44k • written 2 days ago by
biotrekker
▴ 110
0
votes
0
replies
131
views
News:
Online Course: Network Analysis in R (May 5-8)
R
NetworkAnalyis
Tidyverse
2 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
188
views
News:
Short Survey on Genomic Data Management & Analysis Workflows
Analysis
Genomics
updated 2 days ago by
Jeremy Leipzig
23k • written 2 days ago by
QMS
• 0
0
votes
1
reply
170
views
Motif enrichment across super-enhancer regions
motif
HOMER
enrichment
updated 2 days ago by
rfran010
★ 1.3k • written 2 days ago by
SEJAL
• 0
0
votes
0
replies
143
views
JASPAR Database
JASPAR
HOMER
2 days ago by
SEJAL
• 0
1
vote
3
replies
258
views
Finding ORFs in a FASTA file
MatrixScore
ORFs
Motifs
MotifScoring
updated 1 day ago by
Ram
44k • written 3 days ago by
Melissa
• 0
1
vote
1
reply
198
views
How to perform Linkage Disequilibrium (LD) analysis in INDELS
SNPs
PLINK
linkage
disequilibrium
haploview
updated 1 day ago by
dthorbur
★ 2.8k • written 3 days ago by
Ant
▴ 40
0
votes
0
replies
155
views
Spatt2.1 a mirMap dependency, anyone know where I can get it?
miRmap
dependency
tarball
3 days ago by
RNAseqer
▴ 280
0
votes
0
replies
155
views
DeChat Nanopore read correction with Medaka correction?
ont
medaka
wgs
dechat
nanopore
3 days ago by
Mark
▴ 30
0
votes
1
reply
222
views
Why are phenotype values missing in PLINK analysis despite no NA values in the input?
PLINK
PRS
PHS
PGS
SNPanalysis
updated 19 hours ago by
chrchang523
11k • written 3 days ago by
comu
• 0
2
votes
2
replies
341
views
Should I not have any adapters after trimming?
RNA-seq
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
bioinfo
▴ 150
1
vote
3
replies
348
views
Multiple fail points in fastqc file
fastqc
report
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
dr.deepakkukkar
• 0
2
votes
6
replies
440
views
Incorrect gene naming (SYMBOL)
Gene-annotation
updated 1 day ago by
Ram
44k • written 4 days ago by
Biomed-jeh
▴ 70
0
votes
0
replies
228
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 4 days ago by
Ram
44k • written 4 days ago by
s
• 0
1
vote
1
reply
305
views
Problem after subset of single cell integrated dataset in seurat using sctransform
seurat
integration
scRNAseq
sctransform
subset
4 days ago by
NGS_enthusiast
• 0
3
votes
4
replies
414
views
Per Sequence GC Content fail
fastqc
updated 4 days ago by
GenoMax
149k • written 5 days ago by
Eduardo
• 0
2
votes
5
replies
1.4k
views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated 1 day ago by
dthorbur
★ 2.8k • written 4 days ago by
Bruno Santos
• 0
3
votes
5
replies
488
views
Why do people say it doesn't matter whether you run unassembled or assembled reads through Kraken?
assembly
unassembled-reads
Kraken
updated 17 hours ago by
dthorbur
★ 2.8k • written 5 days ago by
trkfs
▴ 10
3
votes
5
replies
378
views
Best way to provide sequences to Local Colabfold to not overload their mmseq2 server
Local
ColabFold
updated 4 days ago by
dthorbur
★ 2.8k • written 4 days ago by
myoui3122010
▴ 30
4
votes
9
replies
581
views
Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda
mamba
repos
miniforge
channels
updated 3 days ago by
Jesse
▴ 850 • written 5 days ago by
kalavattam
▴ 310
3
votes
6
replies
1.0k
views
Tool:
A c library for reading and writing sequences in fasta and fastq format.
seqio
4 days ago by
dwpeng
▴ 110
0
votes
0
replies
219
views
Difference between mutect2 and strelka2
mutect2
strelka2
5 days ago by
ramiro.barrantes
▴ 20
0
votes
1
reply
343
views
GO Analysis Combine or Separate DEGs
clusterProfiler
GO
updated 5 days ago by
mark.ziemann
★ 2.0k • written 7 days ago by
Koki
• 0
120,452 results • Page
1 of 2410
Recent Votes
Comment: Extract FUngal mRNA from RNAseq Data
Comment: Differential Expression and absolute expression
Is there a tool or method for phasing a VCF based on an already phased BAM?
A: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
Answer: Differential Expression and absolute expression
Comment: circos ignoring the ticks and plots
Answer: Split genotypes in VCF file
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Comment: Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing
by
Wu-Sheng Zhang
• 0
Hi @genomax , thank you very much for your help! I go through that page but still a little confused. 10x scMultiomics data would store scAT…
Comment: multiBamSummary
by
JC
13k
check https://broadinstitute.github.io/picard/explain-flags.html to choose a proper flag
Answer: multiBamSummary
by
JC
13k
Yes, `--samFlagExclude 16` will exclude reads in the reverse strand, you need `--samFlagInclude 16` (primary hits, reverse strand) or some …
Answer: Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
by
Mensur Dlakic
★ 29k
While I use Bowtie2, there is not a strong argument for it versus other genome aligners. I guess it is because I found a pipeline back in t…
Comment: How to convert CIGAR string to VCF?
by
cmdcolin
★ 4.1k
i think this is a good exercise (I wrote a quick code that I have used for cigar parsing in javascript https://cmdcolin.github.io/posts/202…
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra
by
Jeremy Leipzig
23k
seqr now fully supports Hail but apparently there are some issues that will force yet another switch https://github.com/broadinstitute/seqr…
Answer: How to convert CIGAR string to VCF?
by
Pierre Lindenbaum
165k
pseudo code: refpos1 = <something-clipped-start> readpos0= 0; for(CigarElement ce: cigar) { char co = ce.getOpera…
Comment: Split genotypes in VCF file
by
Biomonika (Noolean)
3.2k
vt decompose did the trick for me, followed by the filtering for 10th and 11th column. Thanks!
Comment: Extract FUngal mRNA from RNAseq Data
by
GenoMax
149k
Looks good to me. You are being strict with multi-mappers across genomes (i.e. throwing them away). Something to make a note of.
Comment: CLI Downloading from Human Microbiome Project Given Login + contact failure
by
Arup Ghosh
3.3k
Try the [HMP client][1] to download files from their [new portal][2]. [1]: https://github.com/IGS/portal_client [2]: https://portal.h…
Comment: Extract FUngal mRNA from RNAseq Data
by
SomeOne
▴ 170
i used the following command. Kindly let me know if i missed something or if it is now correct ``` bbsplit.sh ref=human_GRCh38.p14_genomic…
Comment: Gini Coefficient and Lorenz curve to measure uniformity of coverage
by
abascalfederico
★ 1.2k
Thank you! I finally used some code from my supervisor for the Lorenz curves, it's relatively easy, and DescTools::Gini to compute the gini…
Comment: Why do people say it doesn't matter whether you run unassembled or assembled rea
by
dthorbur
★ 2.8k
I'm not all that familiar with your field of research, but it would seem counterproductive to try and assemble reads of a microbial communi…
Comment: Extract FUngal mRNA from RNAseq Data
by
GenoMax
149k
It is worth trying. You will know reads that map to the fungal reference (even though fragmented) definitely belong there. You could also…
Comment: Extract FUngal mRNA from RNAseq Data
by
SomeOne
▴ 170
unfortunatly there is no chromosoem level reference genome available. But there are some genome assemblies available at scaffold or contig …
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