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120,738 results • Page
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26
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Beagle Imputation
Beagle
Imputation
3 hours ago by
mahlet.teka
• 0
0
votes
0
replies
24
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep
snpeff
updated 4 hours ago by
GenoMax
150k • written 4 hours ago by
mary.v.volkova
▴ 10
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
70
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount
somaticsniper
updated 4 hours ago by
Pierre Lindenbaum
165k • written 4 hours ago by
1phamcha2
• 0
2
votes
1
reply
56
views
miRNA-seq: QC reports and workflow
miRNA-seq
ION-Torrent
RNA-seq
FASTQC
updated 4 hours ago by
GenoMax
150k • written 5 hours ago by
omicon
▴ 40
1
vote
0
replies
31
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans
Foldseek
Genes
Orthologs
Homologs
5 hours ago by
bioinformatics_rk
▴ 10
0
votes
3
replies
143
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 5 hours ago by
swbarnes2
14k • written 23 hours ago by
Megan
▴ 50
0
votes
0
replies
32
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
6 hours ago by
baibhu1234
▴ 20
0
votes
1
reply
118
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 6 hours ago by
shelkmike
★ 1.5k • written 1 day ago by
Mark
▴ 30
0
votes
1
reply
93
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 6 hours ago by
shelkmike
★ 1.5k • written 11 hours ago by
Ariadna
▴ 20
0
votes
1
reply
101
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
updated 6 hours ago by
jared.andrews07
★ 18k • written 13 hours ago by
Riley J
• 0
2
votes
2
replies
85
views
Population genetics with mutect2 data
haplotypecaller
mutect2
5 hours ago by
slzr_
• 0
1
vote
2
replies
86
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 8 hours ago by
Watermelon
• 0 • written 8 hours ago by
gogeni5529
▴ 60
1
vote
2
replies
126
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 6 hours ago by
Ram
45k • written 14 hours ago by
uttkarsh
• 0
0
votes
0
replies
53
views
Chrom3D
chrom3d
interchromosomal
genome
model
12 hours ago by
desptsp
• 0
0
votes
1
reply
74
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
11 hours ago by
ZheFrench
▴ 590
1
vote
3
replies
121
views
CPTAC Data analysis
CPTAC
proteomics
updated 7 hours ago by
LauferVA
4.5k • written 13 hours ago by
jain72744
▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere
ucsc
updated 6 hours ago by
Ram
45k • written 14.5 years ago by
Jdk
▴ 260
0
votes
3
replies
118
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 15 hours ago by
GenoMax
150k • written 16 hours ago by
omicon
▴ 40
0
votes
3
replies
125
views
Methylation cpg probes annotation
annotation
methylation
cpg
TCGA
updated 11 hours ago by
GenoMax
150k • written 16 hours ago by
jain72744
▴ 10
1
vote
2
replies
235
views
How to convert .ab1 to fastq
Fastq
updated 18 hours ago by
size_t
▴ 120 • written 2 days ago by
dr.suvarnakapale
• 0
1
vote
3
replies
140
views
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 13 hours ago by
colindaven
7.3k • written 18 hours ago by
Shuo
• 0
0
votes
1
reply
103
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
updated 10 hours ago by
dthorbur
★ 2.9k • written 18 hours ago by
v.berriosfarias
▴ 140
0
votes
1
reply
141
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
updated 20 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
100
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
updated 11 hours ago by
dariober
15k • written 21 hours ago by
Jl
• 0
1
vote
2
replies
137
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
10 hours ago by
noodlejackson
▴ 40
0
votes
0
replies
80
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
1 day ago by
emalekos
▴ 40
1
vote
2
replies
132
views
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback
tool
2 hours ago by
genanalyzer24
• 0
1
vote
1
reply
132
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy
RNA-Seq
updated 12 hours ago by
ATpoint
87k • written 1 day ago by
bioinfo1990
• 0
2
votes
1
reply
907
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 1 day ago by
bioinfo_enthusiast
• 0 • written 3.8 years ago by
Kumar
▴ 120
0
votes
0
replies
105
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
2 days ago by
1769mkc
★ 1.2k
0
votes
2
replies
254
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 2 days ago by
dsull
★ 7.3k • written 3 days ago by
brutonk
• 0
0
votes
0
replies
138
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
2 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
245
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
4 hours ago by
ATRX
★ 1.2k
0
votes
1
reply
431
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 3 days ago by
S
• 0 • written 4 weeks ago by
s
• 0
0
votes
0
replies
141
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
1 day ago by
Mllepnos
• 0
2
votes
0
replies
136
views
Tool:
PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment
function
GO
goterms
geneontology
3 days ago by
geneontologyhelp
▴ 460
0
votes
0
replies
148
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
3 days ago by
Ram
45k
2
votes
1
reply
260
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
updated 3 days ago by
grover.sandeep
▴ 20 • written 5 days ago by
s.may-wilson
▴ 50
0
votes
0
replies
150
views
News:
Multi-Omics Integration with Machine Learning — Online Course!
Machine-Learning
Multi-Omics
Depp-Learning
Data-Integration
BigData
3 days ago by
Physalia-courses
★ 2.6k
3
votes
2
replies
246
views
Alignment algorithm for DNA sequencing
sequencing
data
DNA
updated 3 days ago by
ATpoint
87k • written 3 days ago by
QX
▴ 70
0
votes
1
reply
213
views
RepeatMasker UCSC track
RepeatMasker
updated 3 days ago by
Michael
55k • written 3 days ago by
frarodmar17
• 0
0
votes
0
replies
164
views
rarefaction curve metagenomic reads show species saturation around 100 000 reads
metagenomics
rarefaction
kraken2
3 days ago by
rDNA
▴ 20
0
votes
4
replies
484
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 3 days ago by
jared.andrews07
★ 18k • written 6 days ago by
Pumla
• 0
9
votes
21
replies
7.8k
views
12 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 3 days ago by
bagdevi.mishra
▴ 110 • written 6 months ago by
Martina
• 0
0
votes
2
replies
244
views
Looking up gene name from mRNA ID using biomaRt
R
mRNA
biomaRt
updated 3 days ago by
Ram
45k • written 3 days ago by
Khôi
• 0
0
votes
0
replies
182
views
Interpreting negative gap length in MUMMER4
mummer
translocation
3 days ago by
cedric.blais
▴ 20
0
votes
0
replies
163
views
Uncertainty about deepTools computeMatrix options for RNA modifications
deepTools
metagene
computeMatrix
3 days ago by
Kyle
• 0
0
votes
0
replies
158
views
News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
4 days ago by
soledad.esteban
• 0
6
votes
6
replies
574
views
Multiple factors in DESeq2
deseq2
4 days ago by
noodlejackson
▴ 40
120,738 results • Page
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Comment: Adapters, adapters, adapters i´m so confused
Answer: Adapters, adapters, adapters i´m so confused
Comment: Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation
Answer: Gene Expression Timeline Analysis for N=1
A: ATAC-seq sample normalization (quantil normalization)
A: ATAC-seq sample normalization (quantil normalization)
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
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Comment: fastq-dump: command not found, what is wrong?
by
caidyn.c.j
• 0
Hi, I am having this same problem as OP right now. When I do the echo $PATH command, it returns: /Users/chachonos/sratoolkit.3.0.0-ma…
Comment: Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation
by
genanalyzer24
• 0
You're right, thanks for catching that. Here it is: https://genanalyzer.pythonanywhere.com/. Let me know what you think :)
Comment: Gene Expression Timeline Analysis for N=1
by
ATRX
★ 1.2k
Thanks for all the inputs.
Answer: miRNA-seq: QC reports and workflow
by
GenoMax
150k
Since you have publications associated with this data (based on your last thread and a question before that) don't try to do this analysis …
Comment: Population genetics with mutect2 data
by
slzr_
• 0
Thank you so much, you were really helpful! Do you think it is possible to do some kind of analysis to evaluate positive selection or mainl…
Comment: Is there too little variation to detect meaningful gene changes?
by
swbarnes2
14k
I doubt your RNA quality is the issue. It's not likely that poor quality would cause reads to align to the wrong gene. Its far more likely …
Comment: Is there too little variation to detect meaningful gene changes?
by
Megan
▴ 50
The RIN values for these samples ranged around 6.0-7.0, which I think would suggest RNA degradation. From what I am aware of, I don't think…
Answer: Recommendations for Reference-guided de novo assembly assembly approaches or pip
by
shelkmike
★ 1.5k
You can do a de novo assembly and then scaffold the contigs using a reference by RagTag (https://github.com/malonge/RagTag). However, I per…
Answer: Per Base Sequence Content FastQC
by
shelkmike
★ 1.5k
The difference between (A or T) and (G or C) may reflect the GC composition of the genome. Thus, it is not indicative of some sequencing pr…
Answer: Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transc
by
jared.andrews07
★ 18k
What do you mean by "non-raw" data? You're correct in that grabbing arbitrary values on different scales and trying to mash them together i…
Comment: phylogenic analysis
by
Ram
45k
None of the tags you used are relevant to the question you asked - they broadly describe the entire field of bioinformatics. I've fixed it …
Answer: Population genetics with mutect2 data
by
LauferVA
4.5k
Hi @slzr_ In short, no. What I mean is, it’s generally not recommended to use Mutect2 calls directly for classical population genetics ana…
Comment: CPTAC Data analysis
by
LauferVA
4.5k
Please note also that there are also forums that directly relate to CPTAC (only), which may be more appropriate depending on the nature of …
Answer: ggplot of two data set with different colors
by
Watermelon
• 0
Try ggnewscale package, add new_scale_color() between the plots. Something like this should work ggplot() + geom_line(data = gr…
Comment: ggplot of two data set with different colors
by
Arup Ghosh
3.3k
You are trying to colour the same gene names with two different codes. Either make two subplots for the groups or change the shape of dots …
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