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120,183 results • Page
1 of 2404
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News:
Spring School in Bioinformatics - ONLINE, 31 March–4 April 2025
NGS
Phylogenomics
RNAseq
6 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
46
views
How to make a .gaf file for GO analysis
NGS
GO
10 hours ago by
noodle
▴ 620
825
votes
169
replies
164k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.3k • written 8.1 years ago by
Istvan Albert
102k
0
votes
2
replies
135
views
Protein adnotation, gene adnnotation, hordeum vulgare RNA-Seq
protein
vulgare
RNA-Seq
hordeum
gene
updated 19 hours ago by
GenoMax
148k • written 22 hours ago by
martta95
▴ 10
1
vote
1
reply
473
views
On applying spike-in-derived scaling factors to ChIP-seq data: adjust for background signal (input) or not?
spike-in
deepTools
normalization
ChIP-seq
scaling-factor
22 hours ago by
kalavattam
▴ 280
0
votes
3
replies
282
views
WGCNA: Can we use high power for signed network?
Powerselection
RNA-seqdata
WGCNA
Networkanalysis
updated 12 hours ago by
Crystal571
• 0 • written 4 days ago by
Vinesh
▴ 10
0
votes
0
replies
81
views
ChIP-seq signal across bed regions
normalisation
chipseq
quantification
signal
1 day ago by
SEJAL
• 0
1
vote
2
replies
293
views
SRA fastq modify by 10x valid fastq
fastq
1 day ago by
wyuan37
• 0
0
votes
0
replies
101
views
How can I get raw CPTAC protein quantification data ?
CPTAC
proteomics
proteins
python
transcriptome
1 day ago by
AlexStar
▴ 170
0
votes
0
replies
106
views
News:
Workshop: Virtual RNA-seq Analysis, February 4-6
gene
RNASeq
workshop
expression
1 day ago by
spu24005
• 0
0
votes
1
reply
155
views
Integration of Cut&Tag to ATACseq and RNAseq data - impact of a mutation
RNAseq
Cut_Tag
ATACseq
updated 1 day ago by
LChart
4.7k • written 2 days ago by
Alexandre Eeckhoutte
• 0
3
votes
3
replies
905
views
Started running InterProscan locally. Looks like the process isn't progressing well. Can you look at the report?
genome
interproscan
annotation
updated 1 day ago by
Olivier
• 0 • written 3 months ago by
Vijith
▴ 100
0
votes
0
replies
102
views
biomaRt R package
R
biomaRt
transcript_id
ensembl
updated 1 day ago by
Istvan Albert
102k • written 1 day ago by
rajdeepboral00
▴ 20
0
votes
2
replies
381
views
How to Process PacBio RS FASTQ Files from SRA for Genome Coassembly with Illumina Reads?
coassembly
fastq
pacbio
updated 1 day ago by
courtney.stairs
▴ 50 • written 12 weeks ago by
till
• 0
0
votes
0
replies
110
views
How to convert omim database files to annovar compatible
OMIM
WES
Annovar
WGS
2 days ago by
aiswaryabioinfo
▴ 30
1
vote
1
reply
149
views
How can I add new column into Metadata of Seurat.obj in Xenium analysis
seurat
xenium
spatial
transcriptomics
updated 2 days ago by
Bastien Hervé
6.1k • written 2 days ago by
geno89
▴ 10
0
votes
1
reply
521
views
Facing issue while running PHASTEST docker
phage
prophage
phastest
docker
updated 2 days ago by
GenoMax
148k • written 5 weeks ago by
Himu22
• 0
6
votes
1
reply
209
views
FPKM without normalization
FPKM
classification
Normalization
updated 2 days ago by
ATpoint
86k • written 2 days ago by
maryak
▴ 20
0
votes
0
replies
129
views
Abyss output scaffolds.fa file contains kmer sized scaffolds
scaffolds
abyss
2 days ago by
analyst
▴ 50
0
votes
3
replies
245
views
PacBio long read processing
PacBio_sequel_II
long_read
updated 14 hours ago by
GenoMax
148k • written 2 days ago by
Mai.Nabil
• 0
1
vote
4
replies
260
views
16S SILVA with Kraken2 doesn't classfying at species level
Taxonomy
16S
Kraken2
Metagenomics
SILVA
12 hours ago by
Aytaç
• 0
14
votes
12
replies
565
views
What additional info is found in BAM files from PacBio HiFi compared to Fastq files
bam
hifi
fastq
pacbio
updated 2 days ago by
Billy Rowell
▴ 470 • written 3 days ago by
Eric Normandeau
11k
1
vote
3
replies
314
views
Reducing runtime of low-score alignments
python
pairwise-alignment
alignment
updated 2 days ago by
Istvan Albert
102k • written 4 days ago by
benjlishani7
• 0
2
votes
4
replies
355
views
Discover novel transcripts
transcriptomic
assembly
stringtie
stringtie--merge
updated 2 days ago by
Istvan Albert
102k • written 5 days ago by
Emy Alade
• 0
1
vote
3
replies
220
views
bcftools mpileup returns vcf files with only headers
samtools
bcftools
vcf
updated 2 days ago by
DavideSant
• 0 • written 2 days ago by
Brenden
• 0
0
votes
0
replies
126
views
vgconstruct crashes
vg
2 days ago by
Uveyik
▴ 60
1
vote
1
reply
159
views
How to calculate MAF from vcf files ? (SNPVersity from maizeGDB)
SNPs
vcf
MAF
cfR
updated 2 days ago by
Ram
44k • written 3 days ago by
Joséphine
• 0
2
votes
2
replies
206
views
Setting ploidy level in gatk
ploidy
2 days ago by
analyst
▴ 50
0
votes
3
replies
238
views
File h5ad for SEVtras
to
how
updated 2 days ago by
yura.grabovska
▴ 690 • written 3 days ago by
Matteo
• 0
0
votes
2
replies
209
views
chromatin loop annotation for hic
enhancer
chromatin
HI-C
promoter
2 days ago by
J.F.Jiang
▴ 930
0
votes
2
replies
204
views
capmq and verifybamid
bam
capmq
vcf
verifyBAMID
2 days ago by
Peter Chung
▴ 210
0
votes
2
replies
236
views
ribosomeProfilingQC help
ribo-seq
1 day ago by
tommy
▴ 40
0
votes
0
replies
148
views
How to interpret Phylonet MCMC_BiMarkers result file + Running time problem
phylonet
3 days ago by
ylkim9
• 0
0
votes
0
replies
137
views
Converting gaf files to sam/bam?
bam
gaf
sam
3 days ago by
guntul
▴ 40
1
vote
2
replies
280
views
Error from Using FindVariableFeatures Function in Seurat Package
FindVariableFeatures
Seurat
12 hours ago by
Binghong
▴ 20
0
votes
3
replies
278
views
Removing confounding batch effects
sva
limma
batch-effect
2 days ago by
Kaiwen
• 0
0
votes
2
replies
253
views
Best genome assembly tool?
unicycler
assembly
genome
spades
updated 2 days ago by
Istvan Albert
102k • written 3 days ago by
maria.alfarosegura
• 0
1
vote
5
replies
327
views
How to do allele specific expression analysis (ASE)
ASE
updated 3 days ago by
GenoMax
148k • written 3 days ago by
chentongouc
• 0
0
votes
1
reply
212
views
Differentially expressed genes analysis using IPA?
Differential
gene
expression
updated 3 days ago by
ATpoint
86k • written 3 days ago by
goyal.shiwali
▴ 20
0
votes
2
replies
212
views
FilterMutectCalls producing empty vcf file
Mutect2
WES
FilterMutectCalls
gatk
3 days ago by
ChumBucket2024
• 0
3
votes
9
replies
331
views
File size increase after host read removal?
metagenomics
quality-control
WGS
updated 3 days ago by
Ram
44k • written 3 days ago by
akazen
• 0
2
votes
1
reply
211
views
What does the start in diffbind profile plot x-axis mean exactly?
DiffBind
CHiP-Seq
3 days ago by
SpartanII
• 0
0
votes
1
reply
206
views
Disease-Disease Association data
gene-ontology
OMIM
disease
HPO
updated 3 days ago by
Ram
44k • written 4 days ago by
singhankit973
• 0
4
votes
5
replies
381
views
ChromHMM - annotation of chromatin states
state
Annoation
updated 2 days ago by
e.r.zakiev
▴ 230 • written 4 days ago by
Bioinformatics_16
• 0
3
votes
4
replies
298
views
Vcf Filtering
Vcf
Filtering
AF
updated 3 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
Marc Ibanez
• 0
0
votes
0
replies
312
views
News:
Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)
transcriptomics
scRNAseq
singleCell
4 days ago by
ecSeq Bioinformatics
• 0
0
votes
2
replies
3.8k
views
How to Clump In Plink?
PLINK
GWAS
updated 4 days ago by
meggo
• 0 • written 2.6 years ago by
Thorerges
▴ 10
3
votes
8
replies
376
views
Adding p value above plot
p
DESeq2
value
violin
boxplot
updated 3 days ago by
DareDevil
★ 4.3k • written 4 days ago by
a.stef.44
▴ 10
1
vote
1
reply
247
views
Use of Pval v.s. Padj Statistic in Pre-Ranked GSEA Analysis
Gene
Ontology
GSEA
RNA-Seq
updated 4 days ago by
i.sudbery
21k • written 4 days ago by
BioTinker
• 0
0
votes
0
replies
167
views
News:
Online Course: Spatial Omics in R/Bioconductor | 19-21 May 2025
Spatial-Omics
Bioconductor
Tidyverse
Omics
4 days ago by
Physalia-courses
★ 2.6k
120,183 results • Page
1 of 2404
Recent Votes
Answer: Use of Pval v.s. Padj Statistic in Pre-Ranked GSEA Analysis
Sylamer analysis for detecting microRNA binding
Answer: Error from Using FindVariableFeatures Function in Seurat Package
Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr
Answer: How to download FASTQ files from the European Nucleotide Archive (ENA) to use th
Answer: SRA fastq modify by 10x valid fastq
Combining two fasta sequences into one
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Recent Replies
Comment: Error from Using FindVariableFeatures Function in Seurat Package
by
Binghong
▴ 20
Thanks for your guidance, I have a try!
Comment: WGCNA: Can we use high power for signed network?
by
Crystal571
• 0
I used to do that to my TPM, but I got some negative values in my matrix after removebatcheffect. Is that reasonable?
Comment: 16S SILVA with Kraken2 doesn't classfying at species level
by
Aytaç
• 0
I have tried. Problem is in SILVA's naming and coding the seqeunces. They have code and species level in one of their file which is from NC…
Comment: PacBio long read processing
by
GenoMax
148k
ONT has similar workflows. This is probably what you need https://github.com/epi2me-labs/wf-transcriptomes
Comment: Fast, flexible grep for very large FASTQ files
by
milesforjazz
▴ 70
v.1.4.2 introduced the ability to enumerate variants. Read the preprint at **bioRxiv**: https://doi.org/10.1101/2025.01.09.632104
Comment: PacBio long read processing
by
Mai.Nabil
• 0
oh, that's great. I want to do isoform quantification. Also, does Oxford Nanopore have a different workflow?
Answer: Protein adnotation, gene adnnotation, hordeum vulgare RNA-Seq
by
GenoMax
148k
UniProt appears to have proteomes for Barley: https://www.uniprot.org/proteomes/UP000011116 That may be your best bet. They also have GO a…
Comment: Protein adnotation, gene adnnotation, hordeum vulgare RNA-Seq
by
Pierre Lindenbaum
165k
there is a biomart for your genome http://plants.ensembl.org/index.html but I'm afraid the annotation for GO are empty, and KEGG is missing…
Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr
by
kalavattam
▴ 280
Yes, one should account for background signal with input—although many studies do not. For more details, see [Patel et al., The Wild West o…
Comment: 16S SILVA with Kraken2 doesn't classfying at species level
by
noodle
▴ 620
Can you just use nt? Or grab the species level info from nt that you get hits for in the 16S databases and remap? I would expect the 16S d…
Comment: WGCNA: Can we use high power for signed network?
by
ATpoint
86k
18 is below what the authors recommend. TPM has nothing to do with covariantes, and yes you can regress batch from TPM.
Answer: WGCNA: Can we use high power for signed network?
by
Crystal571
• 0
1.I think your deepsplit and minmodulesize are too low. I had 18 samples with 18000 genes and I also used vst and removebatcheffects, but I…
Comment: SRA fastq modify by 10x valid fastq
by
wyuan37
• 0
Thank you! The Data Access is really helpful!
Comment: ribosomeProfilingQC help
by
tommy
▴ 40
Hello, Jack. Thanks for taking the time to answer my question. I believe my dataset should be valid, as I downloaded it directly from [jour…
Answer: Integration of Cut&Tag to ATACseq and RNAseq data - impact of a mutation
by
LChart
4.7k
It seems to me you're thinking mechanistically about this PU.1 mutation. In general it is hard to disentangle direct effects (PU.1 -> Acces…
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