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122,232 results • Page
8 of 2445
Sort: Rank
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Votes
Replies
0
votes
0
replies
514
views
News:
RAD-seq Data Analysis - online course
Phylogenomics
RADseq
Genomics
Population
Stacks
6 weeks ago by
Physalia-courses
★ 2.7k
7
votes
8
replies
2.9k
views
Is there a way to produce/convert nhmmer output to a bed file?
bed
nhmmer
updated 6 weeks ago by
colindaven
8.1k • written 5.1 years ago by
jamie.pike
▴ 90
0
votes
3
replies
799
views
Python deconvolution tools for bulk RNA-seq data
RNA-seq
bulk-rna-seq
Deconvolution
python
transcriptomics
5 weeks ago by
AlexStar
▴ 200
1
vote
1
reply
415
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 6 weeks ago by
GenoMax
154k • written 6 weeks ago by
Kossivi
• 0
2
votes
5
replies
710
views
BWA-MEM with an array of files
alignment
array
BWA-MEM
updated 6 weeks ago by
LChart
5.2k • written 6 weeks ago by
garcesj
▴ 50
0
votes
0
replies
436
views
Job:
Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics
glycoproteomics
proteomics
machine-learning
omics
6 weeks ago by
Daniel
• 0
2
votes
1
reply
520
views
Modeling/simulations using SNPs data
SNP
updated 6 weeks ago by
Dave Carlson
★ 2.2k • written 6 weeks ago by
Gonzalo
• 0
2
votes
1
reply
466
views
Strugling on the 3'rule of HGVS
notation
hgvs
variants
updated 6 weeks ago by
Jeremy Leipzig
23k • written 6 weeks ago by
lacb
▴ 120
13
votes
17
replies
5.3k
views
Extract fastq sequences based on date/time (which is in the header)
sequence
fastq
updated 6 weeks ago by
zhanxw
▴ 20 • written 7.2 years ago by
a.b.g
▴ 10
2
votes
5
replies
3.4k
views
Filter nanopore fastq files by start time
nanopore
fastq
filter
start time
updated 6 weeks ago by
zhanxw
▴ 20 • written 6.4 years ago by
sendhelp
▴ 10
3
votes
4
replies
698
views
Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit
q-score
fastqc
16s-wf
nanoplot
6 weeks ago by
k-tarasov
▴ 10
4
votes
4
replies
937
views
How to create a consensus of a contig with samtools or bbmap?
contig
bbmap
consensus
samtools
genome
updated 6 weeks ago by
jkbonfield
★ 1.3k • written 8 weeks ago by
marongiu.luigi
▴ 770
2
votes
3
replies
714
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq
scRNA-seq
snRNA-seq
updated 6 weeks ago by
ATpoint
90k • written 6 weeks ago by
Ben
• 0
0
votes
2
replies
596
views
What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
7 weeks ago by
fra.r.silvestro
▴ 10
3
votes
1
reply
452
views
Variant Normalization
vcf
updated 7 weeks ago by
Istvan Albert
103k • written 7 weeks ago by
spesks
• 0
1
vote
2
replies
1.0k
views
Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq
DEA
TCGA
Learning
Machine
6 weeks ago by
yordany.perdigon
• 0
0
votes
0
replies
369
views
News:
Autumn School in Bioinformatics – Online, 20–24 October
NGS
Phylogenomics
RNAseq
Singularity
Docker
updated 7 weeks ago by
Pierre Lindenbaum
166k • written 7 weeks ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
456
views
Issue with Snippy 4.6.0
Snippy
Core.vcf
SNP
updated 7 weeks ago by
GenoMax
154k • written 7 weeks ago by
bioinfo_enthusiast
• 0
3
votes
1
reply
519
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 7 weeks ago by
ATpoint
90k • written 7 weeks ago by
carolofharvest
▴ 50
22
votes
13
replies
2.0k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell
software
commercial
gui
7 weeks ago by
firestar
★ 1.7k
1
vote
0
replies
395
views
Tool:
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf
rna-seq
assembly
annotation
transcriptome
7 weeks ago by
Ales
▴ 90
0
votes
2
replies
899
views
scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony
scVI
single
cell
updated 7 weeks ago by
ATpoint
90k • written 7 weeks ago by
biotrekker
▴ 110
1
vote
0
replies
425
views
News:
Manual Genome Curation using PretextView course
Genome-Assembly
PretextView
HI-C
Manuel-Curation
7 weeks ago by
Physalia-courses
★ 2.7k
7
votes
11
replies
1.8k
views
DESeq2 on metagenome KO counts
abundance
KEGG
KO
deseq
metagenome
gene
updated 4 weeks ago by
Aleksandra
▴ 190 • written 7 weeks ago by
young_bioinformatician
▴ 250
0
votes
0
replies
427
views
News:
Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial
Proteomics
omics
updated 7 weeks ago by
GenoMax
154k • written 7 weeks ago by
oliverhooker
▴ 110
2
votes
1
reply
523
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell
rna-detection
FACS
doublet
scRNA-seq
updated 7 weeks ago by
Ram
45k • written 7 weeks ago by
carolofharvest
▴ 50
1
vote
2
replies
722
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools
combine
VCF
updated 21 days ago by
Kevin Blighe
★ 90k • written 7 weeks ago by
Matteo Ungaro
▴ 140
4
votes
4
replies
725
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker
uniprot
proteomics
annotation
trembl
updated 7 weeks ago by
Elisabeth Gasteiger
★ 2.4k • written 7 weeks ago by
Luwell
• 0
7
votes
2
replies
588
views
Recommendations for 200 SNP markers genotyping
sequencing
DNA
genotyping
marker
updated 7 weeks ago by
Aleksandra
▴ 190 • written 7 weeks ago by
PolenP
▴ 10
0
votes
3
replies
708
views
Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run
genomic
features
updated 7 weeks ago by
rfran010
★ 1.7k • written 7 weeks ago by
Rozita
▴ 40
2
votes
6
replies
1.5k
views
Difficulty running FoldX in linux
DDG
foldx
updated 7 weeks ago by
strayeroliver
• 0 • written 7 weeks ago by
strayeroliver
▴ 10
0
votes
2
replies
596
views
Active site using castpfold
activesite
castpfold
Docking
updated 7 weeks ago by
Mensur Dlakic
★ 30k • written 7 weeks ago by
Ria
• 0
5
votes
12
replies
1.7k
views
6 follow
Differences between published differential gene expression results and own analysis on RNA-seq data
R
TCGA
LIMMA
updated 7 weeks ago by
Zhenyu Zhang
★ 1.3k • written 8 weeks ago by
vernonlim98
• 0
0
votes
6
replies
843
views
downloading raw bam files from pacbio sequencer
raw
bam_file
raw_subreads
reads
updated 7 weeks ago by
GenoMax
154k • written 7 weeks ago by
pranavdatar01
• 0
0
votes
2
replies
1.4k
views
Transverse data
EXCEL
Unix
updated 7 weeks ago by
basu
• 0 • written 2.8 years ago by
Sidra
• 0
1
vote
3
replies
631
views
Pseudogene - scarce info
pseudogene
mastersdegree
updated 7 weeks ago by
ATpoint
90k • written 7 weeks ago by
mf810
▴ 10
1
vote
4
replies
2.1k
views
HIV NL4-3 transcriptome fasta
rna-seq
CLIP-seq
updated 7 weeks ago by
Ales
▴ 90 • written 5.7 years ago by
xiaoleiusc
▴ 140
1
vote
1
reply
438
views
Doubt on docking
docking
active-site
updated 6 weeks ago by
Ram
45k • written 7 weeks ago by
Ria
• 0
1
vote
0
replies
390
views
News:
Online course: RNA sequencing data analysis using R and Bioconductor - 3–14 November
R
DifferentialExpressionAnalysis
RNAseq
Bioconductor
7 weeks ago by
Physalia-courses
★ 2.7k
6
votes
3
replies
637
views
Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
fastqc
nextflow
multiqc
updated 7 weeks ago by
Phil Ewels
★ 1.5k • written 8 weeks ago by
DdogBoss
▴ 40
0
votes
2
replies
5.8k
views
Best set of tools / workflows for predicting the biosynthesis pathways of complex organic molecules
ngs
pathways
updated 6 weeks ago by
Ram
45k • written 10 weeks ago by
Mark
▴ 60
12
votes
15
replies
4.2k
views
6 follow
Tools to simulate Illumina short read sequences and ONT long reads with a reference genome
simulate
short-read
updated 6 weeks ago by
Ram
45k • written 9 weeks ago by
PolenP
▴ 10
1
vote
1
reply
476
views
Corresponding BAM files
BAM
SRA
GEO
FASTQ
updated 7 weeks ago by
GenoMax
154k • written 7 weeks ago by
aj123
▴ 140
0
votes
2
replies
2.0k
views
Analyzing CRISPR and RNAi genome wide screens
CRISPR
RNAi
meta analysis
updated 7 weeks ago by
Meisam
▴ 250 • written 7.4 years ago by
spacemorrissey
▴ 280
0
votes
3
replies
3.0k
views
meta data analysis for clustering
meta-analysis
clustering
functional genomics
updated 7 weeks ago by
Meisam
▴ 250 • written 7.8 years ago by
jiwpark00
▴ 230
2
votes
9
replies
3.8k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 7 weeks ago by
Ales
▴ 90 • written 7.5 years ago by
caggtaagtat
★ 1.9k
0
votes
0
replies
384
views
Job:
Postdoctoral Fellowship at the American Museum of Natural History's Richard Gilder Graduate School
Postdoctoral
Fellowship
8 weeks ago by
Info-rggs
▴ 20
0
votes
0
replies
339
views
News:
Autumn School in Bioinformatics - online, 20–24 October
NGS
Phylogenomics
RNAseq
Singularity
Docker
8 weeks ago by
Physalia-courses
★ 2.7k
1
vote
4
replies
1.0k
views
Dorado in PowerShell on Windows
Windows
on
PowerShell
in
Dorado
updated 7 weeks ago by
jared.andrews07
★ 19k • written 8 weeks ago by
sbissi102
▴ 10
1
vote
4
replies
867
views
Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2 or winnowmap?
winnowmap
minimap2
R10.4.1
Nanopore
8 weeks ago by
tungsega
▴ 10
122,232 results • Page
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Answer: Problems in Molecular Docking in Autodock vina
by
Anonsirs
• 0
Try to re run the command by first starting meeko and rdkit . to convert PDB files to PDQT files. It can help vina recognize the atom . a…
Comment: "sortmerna" quitting early--is this is a memory issue?
by
Andrew
• 0
Do you mean the maximum % RAM usage it reaches right before the moment it quits? As I said, the computer has 16 GB RAM, and the run fails w…
Comment: Chip-seq analysis Diffbind
by
Irene
▴ 10
Thank you very much for always answering my doubts and questions. I truly value and appreciate it because it helps me understand the result…
Comment: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
by
firefox91
▴ 10
Many thanks !
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
by
GenoMax
154k
> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA. and > I am trying to determine wheth…
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
by
dthorbur
★ 3.2k
There are a few factors to consider: **The quality of the existing reference.** If there is a high quality chromosome level assembly,…
Comment: "sortmerna" quitting early--is this is a memory issue?
by
colindaven
8.1k
Pls add the output and your system (especially RAM), no one here can guess.
Answer: Power calculations for differentially methylated DNA samples from sequencing
by
colindaven
8.1k
There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
Comment: Data integration single cell using Harmony
by
Arup Ghosh
3.5k
Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
Comment: Data integration single cell using Harmony
by
_deb
• 0
Thank you for the quick answer. I still have a doubt. It would be better to pre-process each sample separately (*filtering, SCTransform…
Comment: Issue while running Kenddata.
by
rana.elromh
• 0
I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
Comment: Prokka output genes clusterization by function
by
Mensur Dlakic
★ 30k
Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
Comment: mapping sequences on specific region of bacteria genome
by
samuel.a.odonnell
▴ 650
If you want to visualise the mapping; take a look at using IGV. It just requires the genome you used to map the reads and the BAM output (n…
Comment: Prokka output genes clusterization by function
by
shevch2009
▴ 20
Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :) I was just trying to figure out how peop…
Answer: Prokka output genes clusterization by function
by
Mensur Dlakic
★ 30k
It is easy to install `kofam_scan` and get the output: https://github.com/takaram/kofam_scan What is the impediment to using METABOLI…
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