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120,397 results • Page
1 of 2408
Sort: Rank
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0
votes
0
replies
36
views
Demultiplexing asymmetrically barcoded reads from multiplex amplicon nanopore sequencing
ONT
demultiplex
4 hours ago by
michael.flower.14
▴ 200
0
votes
1
reply
106
views
Regex in umi-tools doesn't identify pattern in non-beginning positions
whitelist
UMI-Tools
UMI
UMI-TOOLS
umi-tools
updated 5 hours ago by
swbarnes2
14k • written 13 hours ago by
kalaivani
• 0
0
votes
0
replies
50
views
Proteomics Data Analysis
Proteomics
7 hours ago by
frarodmar17
• 0
828
votes
169
replies
166k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
0
replies
57
views
GRCh38 reference paths in human pangenome
HPRC
GRCh38
updated 10 hours ago by
GenoMax
149k • written 10 hours ago by
Rugare
• 0
2
votes
1
reply
91
views
Annotate WGS VCF with Allele Frequencies
snpeff
vcf
wgs
allele
updated 10 hours ago by
Pierre Lindenbaum
165k • written 12 hours ago by
Gabriel
• 0
0
votes
2
replies
135
views
dentifying tumor vs normal cells in spatial transcriptomics
seurat
xenium
spatial-transcriptomics
updated 7 hours ago by
jared.andrews07
★ 18k • written 16 hours ago by
geno89
▴ 10
2
votes
1
reply
770
views
Which zUMIs output to use for differential gene expression?
zumis
rnaseq
smartseq3
single-cell
updated 10 hours ago by
Evlampia
• 0 • written 18 months ago by
firestar
★ 1.6k
0
votes
1
reply
66
views
build a diploid reference using cactus-pangenome pipeline
cactus
pangenome
diploid
graph
vg
updated 10 hours ago by
Dunois
★ 2.9k • written 10 hours ago by
lucianocalderon
▴ 10
0
votes
1
reply
100
views
Bowtie index size / richness matters ?
bowtie
updated 13 hours ago by
colindaven
7.1k • written 16 hours ago by
maschi88
• 0
0
votes
0
replies
57
views
VEP doesn't count CADD
CADD
VEP
annotation
13 hours ago by
balanannie
• 0
6
votes
9
replies
5.1k
views
6 follow
News:
New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
DiffBind
ChIP-seq
deepTools
visualization
ATAC-seq
updated 16 hours ago by
lijiangres
• 0 • written 3.7 years ago by
Rory Stark
★ 2.1k
1
vote
1
reply
95
views
Per tile sequence fails after trimming
fastQC
WES
Sequencing
updated 9 hours ago by
GenoMax
149k • written 17 hours ago by
ijarne
▴ 20
0
votes
0
replies
72
views
Parameters for annotation with maker
Maker
masking
plant
annotation
21 hours ago by
san96
▴ 170
1
vote
4
replies
750
views
CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
deconvolution
RNA-seq
CIBERSORTx
CIBERSORT
updated 21 hours ago by
zhbyrd
• 0 • written 8 months ago by
Mr. George
▴ 10
0
votes
0
replies
111
views
Pipelines/Tools for cleaning UK Biobank data?
UKBiobank
RAP
1 day ago by
Christian
• 0
0
votes
0
replies
95
views
GO Analysis Combine or Separate DEGs
clusterProfiler
GO
1 day ago by
Koki
• 0
0
votes
0
replies
97
views
Key error when using prepDE.py
python
prepDE
stringtie
keyerror
updated 11 hours ago by
WouterDeCoster
47k • written 1 day ago by
mohamadelian1996
• 0
0
votes
2
replies
164
views
How to use harmony with scanpy?
scanpy
harmony
1 day ago by
bioinfo
▴ 150
0
votes
2
replies
152
views
Scdblfinder issue
R
scdblfinder
updated 1 day ago by
Ram
44k • written 1 day ago by
rahma.khoualdia
• 0
0
votes
0
replies
98
views
Repeat Modeler Database Generation
repeat_modeler
repeats
fungi
annotation
genomes
1 day ago by
SomeOne
▴ 170
0
votes
2
replies
154
views
Merging paired-end reads after featureCounts
featureCounts
RNAseq
updated 1 day ago by
ATpoint
86k • written 1 day ago by
n_navy
• 0
1
vote
2
replies
176
views
Proteomics DEA
Proteomics
8 hours ago by
frarodmar17
• 0
0
votes
0
replies
85
views
Difficulty Finding LRR SD and BAF Drift in GenomeStudio 2.0
array
LRR
BAF
genomestudio
snp
1 day ago by
Josephine H.
• 0
4
votes
5
replies
239
views
ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with extsize)
MACS3
BAMPE
BAM
Peakcalling
ATAC-seq
updated 1 day ago by
ATpoint
86k • written 1 day ago by
Manko47
▴ 10
0
votes
1
reply
134
views
LH Sequencing Machine?
fastq
updated 1 day ago by
GenoMax
149k • written 1 day ago by
andrebolerbarros
• 0
5
votes
6
replies
338
views
6 follow
High memory sorting of kmers - best way to use sort
uniq
linux
sort
kmers
updated 1 day ago by
Alex Reynolds
36k • written 2 days ago by
r.ackbersingh
▴ 30
0
votes
0
replies
93
views
News:
Bayesian Data Analysis in R – Online Course (March 3-7)
R
RegressionModeling
Statistics
Byesian
1 day ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
114
views
Age covariate in GWAS
GWAS
1 day ago by
aaaniich
• 0
2
votes
4
replies
790
views
How to completely align chromosomes/scaffolds from de novo genome assemblies using MUMMER or other tools?
visualization
genome
alignment
updated 1 day ago by
christophe.klopp
▴ 20 • written 7 days ago by
Drew
• 0
6
votes
8
replies
526
views
How well was the rRNA depletion for RNA-Seq experiments
contamination
star
rrna
bbduk
ribodetector
updated 1 day ago by
GenoMax
149k • written 13 days ago by
gogeni5529
▴ 60
0
votes
0
replies
112
views
News:
Introduction to Machine Learning with R - online, March 3–7
R
Machine-Learning
omics
Genomics
updated 1 day ago by
Ram
44k • written 1 day ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
141
views
Job:
2025 Summer Internship Opportunity in Computational Biology
intern
1 day ago by
Shicheng Guo
★ 9.6k
3
votes
5
replies
1.4k
views
Tools for fasterq file?
trimming
updated 1 day ago by
AB
▴ 390 • written 2.3 years ago by
shinyjj
▴ 50
4
votes
9
replies
1.7k
views
How to convert fasterq File into fastq files ?
fastq
fasterq
updated 1 day ago by
AB
▴ 390 • written 2.2 years ago by
NikhilP
▴ 20
2
votes
5
replies
216
views
How to extract DEGs from GEO database
extract
DEGs
1 day ago by
harrydo1892
• 0
0
votes
1
reply
172
views
plotProfile Errors of DiffBind
DiffBind
updated 1 day ago by
GenoMax
149k • written 2 days ago by
lijiangres
• 0
10
votes
5
replies
305
views
In silico prediction if a phage can invade a bacterium
phage
bacterium
1 day ago by
A_heath
▴ 170
0
votes
4
replies
3.5k
views
BEAST and BEAGLE installed using conda environment, how to connect?
BEAST
BEAUTI
updated 2 days ago by
sbrobeson
• 0 • written 5.1 years ago by
kabir.deb
▴ 90
1
vote
3
replies
283
views
Dimensionality reduction using RNA and protein expression
dimensionality-reduction
RNA-seq
spatial
updated 2 days ago by
LChart
4.8k • written 3 days ago by
noodlejackson
▴ 20
5
votes
2
replies
594
views
java out of memory error through beagle for imputation
beagle
imputation
java
updated 2 days ago by
Ram
44k • written 9 months ago by
analyst
▴ 60
0
votes
2
replies
373
views
BioPython load/save from SnapGene
biopython
2 days ago by
tada
• 0
1
vote
1
reply
195
views
Herald:
The Biostar Herald for Monday, February 10, 2025
herald
updated 2 days ago by
Bastien Hervé
6.1k • written 2 days ago by
Biostar
3.4k
1
vote
1
reply
269
views
Get bond angles for nucleotides in pdb/cif structure file
cif
cryoEM
pymol
pdb
structure
updated 2 days ago by
dthorbur
★ 2.7k • written 5 days ago by
noodle
▴ 640
4
votes
7
replies
304
views
merging .fastq.gz files results in corrupted files
corrupt
gzip
1 day ago by
rDNA
▴ 20
0
votes
1
reply
167
views
Installing VEP for a Specific Chromosome (e.g., Chromosome 1) is not possible??
VEP
updated 2 days ago by
dthorbur
★ 2.7k • written 2 days ago by
Manuel
▴ 50
0
votes
3
replies
218
views
Blast+ remote search for refseq reference genome
API
refseq
updated 1 day ago by
GenoMax
149k • written 2 days ago by
Chiranth
• 0
0
votes
1
reply
212
views
Finding target for the biologically active compound
target-prediction
updated 2 days ago by
dthorbur
★ 2.7k • written 3 days ago by
Pragya
• 0
0
votes
3
replies
227
views
single-cell transcriptomics and bulk proteomics data integration
integration
omics
data
updated 2 days ago by
AB
▴ 390 • written 2 days ago by
frarodmar17
• 0
1
vote
2
replies
209
views
Split genotypes in VCF file
VCF
genotype
dipcall
2 days ago by
Biomonika (Noolean)
3.2k
120,397 results • Page
1 of 2408
Recent Votes
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
Answer: Nextflow - I/O and index issues
Comment: Per tile sequence fails after trimming
Answer: Annotate WGS VCF with Allele Frequencies
Answer: Annotate WGS VCF with Allele Frequencies
Comment: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
Which zUMIs output to use for differential gene expression?
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Answer: Regex in umi-tools doesn't identify pattern in non-beginning positions
by
swbarnes2
14k
You could try without the discard; the examples in the tutorial (https://umi-tools.readthedocs.io/en/latest/regex.html) only use that when …
Comment: Proteomics DEA
by
frarodmar17
• 0
But resuts are much worse than Wilcoxon test, because most proteins do not follow normal distribution.
Comment: Per tile sequence fails after trimming
by
GenoMax
149k
I suggest you proceed with the analysis. Any oddities like this should be managed by the aligner. If you start seeing any strangeness then …
Answer: Annotate WGS VCF with Allele Frequencies
by
Pierre Lindenbaum
165k
see https://www.biostars.org/p/9465960/ "SnpSift: Annotate vcf file using GNOMAD" or, if you just want the internal AF (in YOUR vcf, not i…
Answer: dentifying tumor vs normal cells in spatial transcriptomics
by
jared.andrews07
★ 18k
A few thoughts and questions. What's your model? Has a mutation been introduced in a specific cell type or lineage? If so, you may be able …
Comment: build a diploid reference using cactus-pangenome pipeline
by
Dunois
★ 2.9k
You'll probably receive quicker help over at the `Cactus` GitHub repository: [https://github.com/ComparativeGenomicsToolkit/cactus/issues][…
Comment: Which zUMIs output to use for differential gene expression?
by
Evlampia
• 0
Hello guys! Is there any feedback on the question above?
Comment: dentifying tumor vs normal cells in spatial transcriptomics
by
Ram
44k
Are you looking to classify human vs mouse cells?
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
by
Juke34
9.1k
I do not know if the problem is related but if your genome is already masked you should let all the option empty: ``` #-----Repeat Masking…
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
by
san96
▴ 170
Thank you @juke34 , I used agat for convert my gtf. Sorry, I have other doubt, I'm starting with plant annotation and I'm using maker for t…
Answer: Bowtie index size / richness matters ?
by
colindaven
7.1k
It is a read multimapping problem - bowtie1 (?) likely considers these repetitive and filters them out. Your mistake was to combine all 3 r…
Comment: How do I use md5sum to check if my .fastq files from SRA Explorer have been down
by
ATpoint
86k
fyi, the SRA-explorer is a third-party tool, not one from NCBI.
Comment: Merging gvcf files between Dragen and other calling tools
by
tacrolimus
▴ 140
Dear Pierre, If one set of gvcf files are ISAAC aligned (>80,000 samples) and the other DRAGEN (100 samples) as discussed above but I hav…
Comment: New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
by
lijiangres
• 0
Hi Rory will you help me out about the plot issue? > dba.plotProfile(dbObj5) Generating report-based DBA object... Generat…
Comment: New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
by
lijiangres
• 0
Hi Rory will you help me out about the plot issue? > dba.plotProfile(dbObj5) Generating report-based DBA object... G…
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