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120,752 results • Page
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Votes
Replies
0
votes
2
replies
54
views
How do I figure out pangenome location of hg38 coordinates?
pangenome
hg38
vg
just now by
a5864557
• 0
1
vote
2
replies
87
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
start
position
end
curation
gene
2 hours ago by
Esra
• 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
0
votes
0
replies
27
views
generating manhattan plot through hail
plot
manhattan
hail
visualizations
gwas
2 hours ago by
nitya
• 0
0
votes
0
replies
37
views
Hard Filtering Differences between WES and WGS
WES
Filtering
Differences
Hard
WGS
4 hours ago by
SIMONE
• 0
0
votes
0
replies
40
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2
single-cell
pseudobulk
4 hours ago by
Aspire
▴ 370
0
votes
0
replies
53
views
OMA use case
oma
omastandalone
2 hours ago by
nmalexan
• 0
0
votes
4
replies
246
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 5 hours ago by
Istvan Albert
102k • written 2 days ago by
Megan
▴ 50
1
vote
2
replies
80
views
nanopore SNV callers returns empty VCF
snv_caller
nanopore
3 hours ago by
Meghan.T
• 0
13
votes
3
replies
1.0k
views
Tutorial:
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda
Anaconda
license
7 hours ago by
Juke34
9.1k
0
votes
0
replies
46
views
How many cells are needed in subcluster to draw conclusions?
immunology
T-cells
scRNA-seq
7 hours ago by
S
• 0
0
votes
1
reply
67
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
updated 5 hours ago by
Istvan Albert
102k • written 8 hours ago by
bioinfo
▴ 150
0
votes
1
reply
57
views
Spam:
yerty rtyrt
rtyrty
ityu
updated 8 hours ago by
Ram
45k • written 9 hours ago by
charlessultan28
0
1
vote
1
reply
112
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria
rnaseq
adapter-trimming
updated 8 hours ago by
Ram
45k • written 14 hours ago by
Davor
• 0
1
vote
2
replies
145
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep
snpeff
updated 11 hours ago by
Jeremy Leipzig
23k • written 1 day ago by
mary.v.volkova
▴ 20
0
votes
1
reply
71
views
How to plot LMER estimate values in heatmap ?
cell
scRNAseq
TF
lmer
transcription
updated 14 hours ago by
ATpoint
87k • written 14 hours ago by
carolofharvest
▴ 50
1
vote
2
replies
549
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
16 hours ago by
ecSeq Bioinformatics
▴ 10
0
votes
1
reply
98
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates
DESeq2
RNA-Seq
updated 10 hours ago by
Ram
45k • written 18 hours ago by
hellothere
• 0
0
votes
1
reply
90
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
bioinformatics
GWAS
genetics
WGS
updated 15 hours ago by
Arup Ghosh
3.3k • written 19 hours ago by
K
• 0
0
votes
1
reply
127
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
baibhu1234
▴ 40
0
votes
0
replies
88
views
Beagle Imputation
Beagle
Imputation
1 day ago by
mahlet.teka
• 0
0
votes
0
replies
208
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount
somaticsniper
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
1phamcha2
• 0
2
votes
2
replies
155
views
miRNA-seq: QC reports and workflow
miRNA-seq
ION-Torrent
RNA-seq
FASTQC
6 hours ago by
omicon
▴ 40
1
vote
0
replies
83
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans
Foldseek
Genes
Orthologs
Homologs
1 day ago by
bioinformatics_rk
▴ 10
0
votes
1
reply
169
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 1 day ago by
shelkmike
★ 1.5k • written 2 days ago by
Mark
▴ 30
0
votes
1
reply
140
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 1 day ago by
shelkmike
★ 1.5k • written 1 day ago by
Ariadna
▴ 20
3
votes
2
replies
198
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
20 hours ago by
Riley J
• 0
2
votes
3
replies
151
views
Population genetics with mutect2 data
haplotypecaller
mutect2
updated 36 minutes ago by
LauferVA
4.5k • written 1 day ago by
slzr_
• 0
1
vote
2
replies
141
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 1 day ago by
Watermelon
• 0 • written 1 day ago by
gogeni5529
▴ 60
1
vote
2
replies
174
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 1 day ago by
Ram
45k • written 1 day ago by
uttkarsh
• 0
0
votes
0
replies
89
views
Chrom3D
chrom3d
interchromosomal
genome
model
1 day ago by
desptsp
• 0
0
votes
1
reply
106
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
1 day ago by
ZheFrench
▴ 590
1
vote
3
replies
164
views
CPTAC Data analysis
CPTAC
proteomics
updated 1 day ago by
LauferVA
4.5k • written 1 day ago by
jain72744
▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere
ucsc
updated 1 day ago by
Ram
45k • written 14.5 years ago by
Jdk
▴ 260
0
votes
3
replies
163
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 1 day ago by
GenoMax
150k • written 1 day ago by
omicon
▴ 40
0
votes
3
replies
169
views
Methylation cpg probes annotation
annotation
methylation
cpg
TCGA
updated 1 day ago by
GenoMax
150k • written 1 day ago by
jain72744
▴ 10
1
vote
2
replies
283
views
How to convert .ab1 to fastq
Fastq
updated 1 day ago by
size_t
▴ 120 • written 3 days ago by
dr.suvarnakapale
• 0
1
vote
3
replies
191
views
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 1 day ago by
colindaven
7.3k • written 1 day ago by
Shuo
• 0
0
votes
1
reply
136
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
updated 1 day ago by
dthorbur
★ 2.9k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
1
reply
180
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
172
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
1 day ago by
Jl
• 0
1
vote
2
replies
179
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
1 day ago by
noodlejackson
▴ 40
0
votes
0
replies
115
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
2 days ago by
emalekos
▴ 40
1
vote
2
replies
211
views
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback
tool
1 day ago by
genanalyzer24
• 0
1
vote
1
reply
167
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy
RNA-Seq
updated 1 day ago by
ATpoint
87k • written 2 days ago by
bioinfo1990
• 0
2
votes
1
reply
943
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 2 days ago by
bioinfo_enthusiast
• 0 • written 3.8 years ago by
Kumar
▴ 120
0
votes
0
replies
137
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
3 days ago by
1769mkc
★ 1.2k
0
votes
2
replies
307
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 3 days ago by
dsull
★ 7.3k • written 4 days ago by
brutonk
• 0
0
votes
0
replies
171
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
3 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
314
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
1 day ago by
ATRX
★ 1.2k
120,752 results • Page
1 of 2416
Recent Votes
Comment: How I can curate all exon start-end positions for 50 genes (to create GTF file)?
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: nanopore SNV callers returns empty VCF
Answer: Adapters, adapters, adapters i´m so confused
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
A: Where can I lookup old merged rsIDs?
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Recent Replies
Comment: Population genetics with mutect2 data
by
LauferVA
4.5k
What is the hypothesis here?
Answer: How do I figure out pangenome location of hg38 coordinates?
by
Jouni Sirén
▴ 540
You can use `vg find` option `-p` / `--path` for that. For example: ``` vg find -p "GRCh38#0#chr12:10000000-10000100" -c 2 -x graph.gbz…
Comment: How I can curate all exon start-end positions for 50 genes (to create GTF file)?
by
Esra
• 0
Thanks for your reply. First of all, I’m sorry if my question is unclear—I’m still a beginner in working with these file formats. From what…
Comment: nanopore SNV callers returns empty VCF
by
Meghan.T
• 0
Thank you so much for your response. I forgot to check the alignment statistics. I assume there were too many mutations during the process,…
Comment: What are the advantages of using the T2T as a reference vs GRCh38 today?
by
LauferVA
4.5k
@gordonsmyth returning almost 2 years later to tell you how often i have found it useful to revist this work. thank you
Answer: Is there too little variation to detect meaningful gene changes?
by
Istvan Albert
102k
The problem is not necessarily that there is too little variation - we can't tell how much variation is because the plot is about percenta…
Answer: nanopore SNV callers returns empty VCF
by
Istvan Albert
102k
well it looks like almost no reads aligned, out of 13K reads you have only a single primary alignment hence the variant callers are unab…
Comment: Question about assigning gene names, tximport and DESeq2
by
Istvan Albert
102k
we can't tell what is wrong without seeing the code, but it makes little sense to have an empty gene name row, for genes without a extern…
Comment: miRNA-seq: QC reports and workflow
by
omicon
▴ 40
GenoMax, thank you for your answer. You are correct; the ION-Torrent data comes from the second paper you mentioned, but it was not sequenc…
Answer: Avoiding the Pitfalls of the Anaconda License: A Practical Guide
by
Juke34
9.1k
Pixi has now been added to this documentation!
Comment: How I can curate all exon start-end positions for 50 genes (to create GTF file)?
by
GenoMax
150k
You will likely want to use AGAT toolkit. https://agat.readthedocs.io/en/latest/tools/agat_convert_bed2gff.html <!-- this is it -->
Answer: RNASeq: Confused about adapters with barcodes and seq company's filtering
by
GenoMax
150k
> Illumina Universal Adapter and PolyG, Poly-G are a common observation with 2-color chemistry (where no signal is equated to G). These …
Answer: VEP won't show symbols for all variants; SnpEff will, but won't for others
by
Jeremy Leipzig
23k
This is probably more to do with the gene models being used and certain rules for precedence that each annotator is using. Looks like one o…
Comment: How to plot LMER estimate values in heatmap ?
by
ATpoint
87k
Some might know what "lmer model" for "transcriotion factor analysis" is. Why don't you show representative data so people can suggest visu…
Comment: Differential methylation rate analysis using modkit for m6A
by
doramora
▴ 10
Hi! Why did you want to make a 20 reads threashold? (*Nvalid_cov" as >=20 reads) Are you making any filtering for percent modified ((Nmod /…
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