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120,767 results • Page
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0
votes
0
replies
9
views
Tool for automatic immune cell annotation in MOUSE?
immune
single-cell
annotation
23 minutes ago by
txema.heredia
▴ 210
4
votes
12
replies
6.9k
views
12 follow
How to draw venn diagram for two CNV lists?
venn
updated 44 minutes ago by
5heikki
11k • written 10.3 years ago by
lyz10302012
▴ 480
0
votes
1
reply
24
views
merging diploid and tetraploid vcfs
bcftools
diploid
tetraploid
updated 46 minutes ago by
colindaven
7.3k • written 1 hour ago by
analyst
▴ 60
0
votes
0
replies
20
views
TMM normalized CPM
TPM
CPM
TMM
2 hours ago by
maryak
▴ 20
0
votes
3
replies
96
views
Downloading full list of Homo sapiens genes
Genes
updated 3 hours ago by
GenoMax
150k • written 8 hours ago by
nigussie.amu
• 0
0
votes
0
replies
31
views
Normlizatiom in DiffBind
DiffBind
CHIP-Seq
5 hours ago by
Siqi
• 0
0
votes
1
reply
58
views
Obtain genome coordinates for a DNA sequence using ENSEMBL API
Ensembl
API
updated 6 hours ago by
GenoMax
150k • written 8 hours ago by
Ishan
• 0
0
votes
0
replies
43
views
Forum:
Decoding Corvid Intelligence: Genomics, AI & the Genetics of Cognition
neurogenetics
comparative-genomics
bioinformatics
genomics
machine-learning
updated 7 hours ago by
Ram
45k • written 8 hours ago by
EvoGenExplorer
• 0
2
votes
3
replies
139
views
GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ from GFA
vg
updated 6 hours ago by
Jouni Sirén
▴ 580 • written 14 hours ago by
Sauers
• 0
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
4
votes
14
replies
342
views
6 follow
prokka with too many "hypothetical proteins" and genome comparison
comparison
genome
galaxy
prokka
updated 6 hours ago by
GenoMax
150k • written 21 hours ago by
avinci1
▴ 20
0
votes
1
reply
115
views
Split paired ended hWGS FASTq files to simulate difference sequence coverage
whole-genome-sequencing
wgs
FASTQ
coverage
updated 15 hours ago by
shelkmike
★ 1.5k • written 1 day ago by
DJBill
▴ 20
0
votes
1
reply
135
views
OMA use case
oma
omastandalone
updated 15 hours ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
nmalexan
• 0
0
votes
0
replies
56
views
News:
Machine Learning for Longitudinal Data with Python – Online Course (6-9 May)
MachineLearning
LongitudinalData
DeepLearning
Omics
16 hours ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
100
views
Recommended workflow to pre-process and demultiplex scRNAseq data based on the HTOs and ADTs
ADT
HTO
demultiplexing
scRNAseq
58 minutes ago by
mete.han.celebi
• 0
0
votes
3
replies
121
views
bwa-mem keeps failing to locate the index files
bwa
bwa-mem
updated 17 hours ago by
ATpoint
87k • written 18 hours ago by
pairedttest
▴ 30
1
vote
5
replies
293
views
6 follow
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 16 hours ago by
Joe
22k • written 3 days ago by
Shuo
• 0
0
votes
0
replies
54
views
Olink - OlinkAnalyze Package - olink_umap_plot function
Olink
proteomics
18 hours ago by
kristina
• 0
2
votes
0
replies
76
views
Herald:
The Biostar Herald for Wednesday, March 19, 2025
herald
19 hours ago by
Biostar
3.4k
0
votes
0
replies
66
views
Cosmic database update issue in annovar
annovar
cosmic
genomics
updated 18 hours ago by
Ram
45k • written 22 hours ago by
abhijitswain
• 0
1
vote
1
reply
237
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF
genotype
gVCF
22 hours ago by
Michaela
▴ 10
3
votes
2
replies
185
views
How do I figure out pangenome location of hg38 coordinates?
pangenome
hg38
vg
1 day ago by
a5864557
▴ 10
1
vote
4
replies
219
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
gtf
curation
gene
updated 18 hours ago by
Ram
45k • written 1 day ago by
Esra
• 0
0
votes
0
replies
84
views
generating manhattan plot through hail
plot
manhattan
hail
visualizations
gwas
1 day ago by
nitya
• 0
0
votes
0
replies
86
views
Hard Filtering Differences between WES and WGS
WES
WGS
Hard-Filtering
updated 18 hours ago by
Ram
45k • written 1 day ago by
SIMONE
• 0
0
votes
3
replies
188
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2
single-cell
pseudobulk
updated 20 hours ago by
ATpoint
87k • written 1 day ago by
Aspire
▴ 370
2
votes
4
replies
322
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 1 day ago by
Istvan Albert
102k • written 3 days ago by
Megan
▴ 50
2
votes
4
replies
206
views
nanopore SNV callers returns empty VCF
snv_caller
nanopore
4 hours ago by
Meghan.T
• 0
14
votes
3
replies
1.1k
views
Tutorial:
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda
Anaconda
license
14 hours ago by
Juke34
9.2k
0
votes
1
reply
124
views
How many cells are needed in subcluster to draw conclusions?
immunology
T-cells
scRNA-seq
updated 23 hours ago by
ATpoint
87k • written 1 day ago by
S
• 0
0
votes
1
reply
124
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
updated 1 day ago by
Istvan Albert
102k • written 1 day ago by
bioinfo
▴ 150
2
votes
3
replies
211
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria
rnaseq
adapter-trimming
updated 5 hours ago by
GenoMax
150k • written 1 day ago by
Davor
• 0
1
vote
2
replies
190
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep
snpeff
updated 1 day ago by
Jeremy Leipzig
23k • written 2 days ago by
mary.v.volkova
▴ 20
0
votes
2
replies
134
views
How to plot LMER estimate values in heatmap ?
cell
scRNAseq
TF
lmer
transcription
17 hours ago by
carolofharvest
▴ 50
1
vote
2
replies
811
views
News:
Final Call - Next-Generation Sequencing Data Analysis: A Practical Introduction (April 2-4 in Munich) - Only 2 seats left
Workshop
RNAseq
Variant-Calling
Illumina
DNAseq
1 day ago by
ecSeq Bioinformatics
▴ 10
0
votes
1
reply
131
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates
DESeq2
RNA-Seq
updated 1 day ago by
Ram
45k • written 2 days ago by
hellothere
• 0
0
votes
2
replies
146
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
bioinformatics
GWAS
genetics
WGS
3 hours ago by
K
• 0
0
votes
1
reply
171
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
updated 2 days ago by
i.sudbery
21k • written 2 days ago by
baibhu1234
▴ 40
0
votes
0
replies
123
views
Beagle Imputation
Beagle
Imputation
2 days ago by
mahlet.teka
• 0
0
votes
0
replies
243
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount
somaticsniper
updated 2 days ago by
Pierre Lindenbaum
165k • written 2 days ago by
1phamcha2
• 0
2
votes
2
replies
217
views
miRNA-seq: QC reports and workflow
miRNA-seq
ION-Torrent
RNA-seq
FASTQC
1 day ago by
omicon
▴ 40
1
vote
0
replies
117
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans
Foldseek
Genes
Orthologs
Homologs
2 days ago by
bioinformatics_rk
▴ 10
0
votes
1
reply
202
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 2 days ago by
shelkmike
★ 1.5k • written 3 days ago by
Mark
▴ 30
0
votes
1
reply
180
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 2 days ago by
shelkmike
★ 1.5k • written 2 days ago by
Ariadna
▴ 20
3
votes
2
replies
242
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
2 days ago by
Riley J
• 0
2
votes
3
replies
223
views
Population genetics with mutect2 data
haplotypecaller
mutect2
updated 1 day ago by
LauferVA
4.6k • written 2 days ago by
slzr_
• 0
1
vote
2
replies
187
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 2 days ago by
Watermelon
• 0 • written 2 days ago by
gogeni5529
▴ 60
1
vote
2
replies
214
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 2 days ago by
Ram
45k • written 3 days ago by
uttkarsh
• 0
0
votes
0
replies
120
views
Chrom3D
chrom3d
interchromosomal
genome
model
2 days ago by
desptsp
• 0
0
votes
1
reply
143
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
2 days ago by
ZheFrench
▴ 590
120,767 results • Page
1 of 2416
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Comment: Recommended workflow to pre-process and demultiplex scRNAseq data based on the H
Comment: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr
Comment: Software for visualizing mass spectromety spectra
Comment: nanopore SNV callers returns empty VCF
Answer: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr
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Recent Replies
Comment: merging diploid and tetraploid vcfs
by
colindaven
7.3k
How are you calling tetraploid variants out of interest ?
Answer: How to draw venn diagram for two CNV lists?
by
5heikki
11k
[This][1] is my favorite online tool for list comparisons [1]: https://molbiotools.com/listcompare.php
Comment: Recommended workflow to pre-process and demultiplex scRNAseq data based on the H
by
mete.han.celebi
• 0
Thank you very much! Yes I haven't seen this. That is very valuable!
Answer: Downloading full list of Homo sapiens genes
by
GenoMax
150k
If you prefer using a GUI interface then visit: https://www.ncbi.nlm.nih.gov/datasets/gene/taxon/9606/ Click on `Select Columns` and then …
Comment: Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
by
K
• 0
thank you, do you have any scripts/commands for converting it to vcf files? i used "gffread input.gvf -T -o output.vcf" but i cannot sort t…
Comment: Downloading full list of Homo sapiens genes
by
GenoMax
150k
If you just need the list of currently approved human genes/symbols you can get that from HGNC/HUGO: https://www.genenames.org/download/sta…
Comment: nanopore SNV callers returns empty VCF
by
Meghan.T
• 0
Thank you so much for your comprehensive response and tips. I reached out to the person who designed the experiment and turns out that the …
Comment: RNASeq: Confused about adapters with barcodes and seq company's filtering
by
GenoMax
150k
Correct. You can specify the core sequence like you did. Once trimming programs find that sequence they will remove all sequence on 3’-side…
Answer: Obtain genome coordinates for a DNA sequence using ENSEMBL API
by
GenoMax
150k
If you are using linux (and are not from a for-profit or industrial institution) you can set up `gfServer/gfclient` locally to do multiple …
Comment: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr
by
Jouni Sirén
▴ 580
The HPRC v1.0 PGGB graph is an old graph, from before path naming conventions were fully established (see [the vg wiki][1]). The full name…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
GenoMax
150k
> So I have all these files for both genomes But you left out an important answer. How many pieces (contigs) are there per genome? Is it a…
Answer: Downloading full list of Homo sapiens genes
by
Sauers
• 0
Not sure about the GSEA database in particular, but for the rest, you may be looking for one of these links: https://ftp.ebi.ac.uk/pub/dat…
Comment: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr
by
Sauers
• 0
Interestingly, I redownloaded the file and got a different error. Before re-downloading, I saw lots of print outputs referring to jobs of …
Answer: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr
by
Jouni Sirén
▴ 580
GBWT construction partitions the graph into weakly connected components. Then it forms construction jobs that consist of one or more compon…
Comment: prokka with too many "hypothetical proteins" and genome comparison
by
Dunois
★ 2.9k
You are welcome. I wish you good luck!!
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