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122,036 results • Page
1 of 2441
Sort: Rank
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Votes
Replies
4
votes
4
replies
523
views
SNP calling ONT sequenced files
ONT
SNPs
updated 26 minutes ago by
Момчил
▴ 10 • written 9 days ago by
blur
▴ 280
0
votes
0
replies
35
views
News:
RAD-seq Data Analysis - online course
Phylogenomics
RADseq
Genomics
Population
Stacks
4 hours ago by
Physalia-courses
★ 2.7k
0
votes
0
replies
48
views
Error "no rows to aggregate" using makeFunctionalPrediction() Tax4fun2
R
Tax4fun2
prediction
functional
makeFunctionalPrediction
7 hours ago by
Marine
• 0
7
votes
8
replies
2.4k
views
Is there a way to produce/convert nhmmer output to a bed file?
bed
nhmmer
updated 11 hours ago by
colindaven
8.0k • written 5.0 years ago by
jamie.pike
▴ 90
0
votes
2
replies
157
views
Python deconvolution tools for bulk RNA-seq data
RNA-seq
bulk-rna-seq
Deconvolution
python
transcriptomics
updated 12 hours ago by
Arup Ghosh
3.4k • written 23 hours ago by
AlexStar
▴ 200
847
votes
170
replies
216k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
training
updated 16 days ago by
Biostar
3.6k • written 8.9 years ago by
Istvan Albert
103k
1
vote
1
reply
121
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 1 day ago by
GenoMax
154k • written 1 day ago by
Kossivi
• 0
2
votes
5
replies
213
views
BWA-MEM with an array of files
alignment
array
BWA-MEM
updated 1 day ago by
LChart
5.1k • written 1 day ago by
garcesj
▴ 50
1
vote
6
replies
232
views
reference-guided assembly tools for short read data?
genomics
assembly
bioinformatics
updated 11 hours ago by
lieven.sterck
16k • written 1 day ago by
Hani
• 0
0
votes
0
replies
90
views
interpretation of the results obtained with digital PCR
dPCR
1 day ago by
Lorenzo
• 0
1
vote
4
replies
218
views
MOuse Testis Enhancer region
enhancer
updated 8 hours ago by
GenoMax
154k • written 1 day ago by
Bioinformatics_16
• 0
0
votes
0
replies
119
views
Job:
Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics
glycoproteomics
proteomics
machine-learning
omics
1 day ago by
Daniel
• 0
2
votes
1
reply
186
views
Modeling/simulations using SNPs data
SNP
updated 1 day ago by
Dave Carlson
★ 2.2k • written 1 day ago by
Gonzalo
• 0
2
votes
1
reply
180
views
Strugling on the 3'rule of HGVS
notation
hgvs
variants
updated 2 days ago by
Jeremy Leipzig
23k • written 2 days ago by
lacb
▴ 120
13
votes
17
replies
4.9k
views
Extract fastq sequences based on date/time (which is in the header)
sequence
fastq
updated 2 days ago by
zhanxw
▴ 20 • written 7.1 years ago by
a.b.g
▴ 10
2
votes
5
replies
3.0k
views
Filter nanopore fastq files by start time
nanopore
fastq
filter
start time
updated 2 days ago by
zhanxw
▴ 20 • written 6.3 years ago by
sendhelp
▴ 10
1
vote
3
replies
343
views
Choosing enrichment analysis tool
DAVID
Metascape
Enrichr
updated 2 days ago by
i.sudbery
22k • written 4 days ago by
Marlene
• 0
3
votes
4
replies
224
views
Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit
q-score
fastqc
16s-wf
nanoplot
2 days ago by
k-tarasov
▴ 10
4
votes
4
replies
586
views
How to create a consensus of a contig with samtools or bbmap?
contig
bbmap
consensus
samtools
genome
updated 2 days ago by
jkbonfield
★ 1.3k • written 13 days ago by
marongiu.luigi
▴ 770
1
vote
1
reply
207
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq
scRNA-seq
snRNA-seq
updated 2 days ago by
ATpoint
89k • written 2 days ago by
Ben
• 0
0
votes
1
reply
153
views
Configuration file for DSP WTA
DSP
updated 2 days ago by
GenoMax
154k • written 2 days ago by
Petesview
▴ 10
0
votes
0
replies
114
views
News:
1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics
RNA-Seq
Expression
Differential
2 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
2
replies
245
views
What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
2 days ago by
fra.r.silvestro
▴ 10
0
votes
0
replies
153
views
Does the weights file stay the same for a different model organism
machine
learning
weights
bioinformatics
updated 2 days ago by
GenoMax
154k • written 3 days ago by
Sharma
• 0
0
votes
2
replies
233
views
HDOCK Server Error!
HDOCK
Docking
17 hours ago by
Jannatul Ferdous
• 0
3
votes
1
reply
198
views
Variant Normalization
vcf
updated 3 days ago by
Istvan Albert
103k • written 3 days ago by
spesks
• 0
1
vote
2
replies
584
views
Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq
DEA
TCGA
Learning
Machine
2 days ago by
yordany.perdigon
• 0
0
votes
0
replies
159
views
News:
Autumn School in Bioinformatics – Online, 20–24 October
NGS
Phylogenomics
RNAseq
Singularity
Docker
updated 3 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
205
views
Issue with Snippy 4.6.0
Snippy
Core.vcf
SNP
updated 3 days ago by
GenoMax
154k • written 3 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
258
views
Cells from normal sample were incorrectly classified as tumor cells using copykat
copykat
scRNA-seq
cell
tumor
1 day ago by
tujuchuanli
▴ 130
0
votes
1
reply
207
views
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
mitochondria
Assembly
Genome
Novoplasty
updated 3 days ago by
GenoMax
154k • written 3 days ago by
Buddha
• 0
3
votes
1
reply
273
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 4 days ago by
ATpoint
89k • written 4 days ago by
carolofharvest
▴ 50
20
votes
13
replies
1.3k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell
software
commercial
gui
4 days ago by
firestar
★ 1.7k
1
vote
0
replies
220
views
Tool:
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf
rna-seq
assembly
annotation
transcriptome
4 days ago by
Ales
▴ 90
0
votes
10
replies
715
views
Tool:
Brave: Bioinformatics Reactive Analysis and Visualization Engine
Docker
R
Nextflow
Python
React
1 day ago by
Edward
• 0
0
votes
2
replies
506
views
scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony
scVI
single
cell
updated 5 days ago by
ATpoint
89k • written 9 days ago by
biotrekker
▴ 110
1
vote
0
replies
249
views
News:
Manual Genome Curation using PretextView course
Genome-Assembly
PretextView
HI-C
Manuel-Curation
6 days ago by
Physalia-courses
★ 2.7k
4
votes
11
replies
902
views
DESeq2 on metagenome KO counts
abundance
KEGG
KO
deseq
metagenome
gene
updated 5 days ago by
Aleksandra
▴ 190 • written 7 days ago by
young_bioinformatician
▴ 240
0
votes
0
replies
287
views
News:
Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial
Proteomics
omics
updated 6 days ago by
GenoMax
154k • written 7 days ago by
oliverhooker
▴ 110
2
votes
1
reply
339
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell
rna-detection
FACS
doublet
scRNA-seq
updated 3 days ago by
Ram
45k • written 7 days ago by
carolofharvest
▴ 50
1
vote
1
reply
404
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools
combine
VCF
updated 5 days ago by
cmdcolin
★ 4.3k • written 7 days ago by
Matteo Ungaro
▴ 130
4
votes
4
replies
468
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker
uniprot
proteomics
annotation
trembl
updated 7 days ago by
Elisabeth Gasteiger
★ 2.4k • written 7 days ago by
Luwell
• 0
7
votes
2
replies
392
views
Recommendations for 200 SNP markers genotyping
sequencing
DNA
genotyping
marker
updated 7 days ago by
Aleksandra
▴ 190 • written 7 days ago by
PolenP
▴ 10
0
votes
3
replies
493
views
Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run
genomic
features
updated 5 days ago by
rfran010
★ 1.7k • written 9 days ago by
Rozita
▴ 40
0
votes
4
replies
491
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end
fastq
paired
updated 13 hours ago by
ATpoint
89k • written 7 days ago by
aj123
▴ 130
1
vote
2
replies
391
views
Reasonable number of SNPs in a bacterial genome.
SNP
bacteria
updated 4 days ago by
michael.ante
★ 4.0k • written 7 days ago by
yesquokkan
• 0
2
votes
6
replies
796
views
Difficulty running FoldX in linux
DDG
foldx
updated 7 days ago by
strayeroliver
• 0 • written 9 days ago by
strayeroliver
▴ 10
0
votes
2
replies
420
views
Active site using castpfold
activesite
castpfold
Docking
updated 7 days ago by
Mensur Dlakic
★ 30k • written 8 days ago by
Ria
• 0
5
votes
12
replies
1.3k
views
6 follow
Differences between published differential gene expression results and own analysis on RNA-seq data
R
TCGA
LIMMA
updated 8 days ago by
Zhenyu Zhang
★ 1.3k • written 15 days ago by
vernonlim98
• 0
1
vote
4
replies
555
views
Problems with PacBio's Improved Phased Assembler (IPA)
pacbio
hifi
assembly
genome
7 days ago by
Panos
★ 1.8k
122,036 results • Page
1 of 2441
Recent Votes
A: Get chromosome sizes from fasta file
How to keep the top hits only in the output file of hmmscan?
A: How to keep the top hits only in the output file of hmmscan?
ProbeID to Gene Symbol Mapping in Microarray data analysis using R
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
Answer: Choosing enrichment analysis tool
Answer: reference-guided assembly tools for short read data?
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▴ 200
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Recent Replies
Answer: SNP calling ONT sequenced files
by
Момчил
▴ 10
Yes, one can say that ONT reads do still have higher error rates in comparison to Illumina short reads, but the situation has improved sign…
Comment: MOuse Testis Enhancer region
by
GenoMax
154k
That web site is off-line for everyone. You will have to look for an alternate option.
Answer: Is there a way to produce/convert nhmmer output to a bed file?
by
colindaven
8.0k
To make it a bit clearer for nhmmer specifically, I used the following. This is code used in nextflow. # run nhmmer nhmm…
Comment: reference-guided assembly tools for short read data?
by
lieven.sterck
16k
there are several options to choose from, doing a quick google search will give you a lot. The main thing to keep in mind is to choose one …
Comment: Python deconvolution tools for bulk RNA-seq data
by
Arup Ghosh
3.4k
Check the [Bulk2Single][1] option from [OmicVerse][2] framework. [1]: https://omicverse.readthedocs.io/en/latest/Tutorials-bulk2single/…
Comment: reference-guided assembly tools for short read data?
by
michael.ante
★ 4.0k
I don't know how well it works for plants, but I worked with [Saute][1] and it was doing well for reference based assemblies. [1]: http…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
ATpoint
89k
Most likely a download artifact. First I would re-download and inly if that fails again then do repairing. ftp is primitive, it's just hit …
Answer: Python deconvolution tools for bulk RNA-seq data
by
ATpoint
89k
Imo you are approaching this the wrong way. R packages for deconvolution that are heqavily used and cited do exist, for example MuSiC and B…
Comment: MOuse Testis Enhancer region
by
Bioinformatics_16
• 0
@genomax Do you have access to this list? If so, could you please share it? I need it urgently.
Comment: HDOCK Server Error!
by
Jannatul Ferdous
• 0
Tried that but unfortunately, the problem still persists :( Thanks for your response though!
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
by
LChart
5.1k
While Himar1 inserts in TA motifs, the library is generated following restriction enzyme treatment (Mmrl) and ligation. The Mmrl sequence i…
Comment: Is it possible to do standard GSEA in R?
by
mbramble
• 0
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
Comment: BWA-MEM with an array of files
by
LChart
5.1k
For solution 1, because bwa streams the data, you can save some space by using a named pipe: ```bash mkfifo Sample_23/concat.R1.fq.gz find…
Comment: reference-guided assembly tools for short read data?
by
Hani
• 0
Either de novo or reference based genome assembly using Illumina PE short reads
Comment: reference-guided assembly tools for short read data?
by
lieven.sterck
16k
which purpose specifically?
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