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121,096 results • Page
1 of 2422
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Votes
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0
votes
0
replies
15
views
Warning in bcftools when subsetting a VCF by variant ID
bcftools
Beagle5.5
VCF
1 hour ago by
Mwangana
• 0
1
vote
2
replies
101
views
Lucidea Array Spotter - Question about machinery
sequencing
Microarray
updated 1 hour ago by
GenoMax
151k • written 6 hours ago by
Taylor
• 0
2
votes
2
replies
105
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 6 hours ago by
GenoMax
151k • written 8 hours ago by
vikasmh111
• 0
0
votes
3
replies
144
views
Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot
PCA
Seurat
scater
single-cell
updated 4 hours ago by
Bastien Hervé
6.2k • written 10 hours ago by
txema.heredia
▴ 210
1
vote
1
reply
93
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 4 hours ago by
GenoMax
151k • written 14 hours ago by
Ambuj
• 0
0
votes
3
replies
159
views
How can I find KO IDs for ORF sequences in a large FASTA file?
KEGG
ORF
updated 3 hours ago by
Ram
45k • written 21 hours ago by
Nikesh
• 0
836
votes
170
replies
175k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
0
replies
76
views
Single MAG Recruitment to multiple metaT Samples
metagenomics
rna-seq
transcriptomics
21 hours ago by
zjhennin
• 0
0
votes
1
reply
914
views
Normalization - Tissue specificity analysis
gtex
updated 22 hours ago by
Pallavi
• 0 • written 4.1 years ago by
Filago
▴ 100
2
votes
4
replies
2.9k
views
Transcript Specific Expression Data
rna-seq
updated 22 hours ago by
Pallavi
• 0 • written 12.5 years ago by
disco
▴ 30
9
votes
6
replies
7.8k
views
6 follow
Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
transcript
updated 22 hours ago by
Pallavi
• 0 • written 12.2 years ago by
michealsmith
▴ 800
6
votes
5
replies
1.9k
views
Tool:
Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
containers
docker
updated 1 day ago by
GenoMax
151k • written 6.2 years ago by
pegi3sdocker
▴ 10
1
vote
0
replies
115
views
Job:
Looking for a mentor
health
mentor
informatics
updated 1 day ago by
GenoMax
151k • written 1 day ago by
yoav.lama
▴ 10
0
votes
0
replies
112
views
Job:
Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
proteomics
genetics
cell
single
bioinformatics
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Jingwen
• 0
0
votes
0
replies
94
views
Strand bias and placement bias in variant calls
Variant
filter
updated 1 day ago by
Pierre Lindenbaum
166k • written 1 day ago by
Carolyn
• 0
0
votes
0
replies
102
views
STARsolo for multiome GEX: trimming (--clip5pNbases) & whitelist handling
STARSolo
multiome
whitelist
clip5pNbases
1 day ago by
IrK
▴ 100
1
vote
8
replies
312
views
Featurecounts: Unexpected number of features
featurecounts
1 day ago by
JourneyToAbyss
▴ 240
4
votes
13
replies
10k
views
7 follow
GVSA: problem with gene identifier
gvsa
RNA-Seq
gsea
updated 1 day ago by
Saravana
• 0 • written 8.0 years ago by
cmgraef
▴ 10
0
votes
0
replies
100
views
News:
Workshop: Virtual Variant Detection, May 20-22
VariantDetection
Workshop
UConn
1 day ago by
zsc25001
• 0
0
votes
0
replies
108
views
Plink vcf file output reporting
vcf
1 day ago by
1769mkc
★ 1.3k
1
vote
3
replies
240
views
Best way to combine biological replicate peaks?
ATAC-seq
updated 2 days ago by
jared.andrews07
★ 18k • written 2 days ago by
SpartanII
• 0
1
vote
5
replies
261
views
Filtering HMMSCAN Domtblout Output when using Metagenomic Sequence as Input
hmmscan
sequences
domtblout
metagenomic
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Jane123
• 0
0
votes
1
reply
171
views
I have doubts regarding conducting meta-analysis of differentially expressed genes
meta-analysis
Differential-Gene-Expression
updated 2 days ago by
LChart
4.9k • written 2 days ago by
Rohan
• 0
0
votes
3
replies
205
views
Create local Blast database alias with blastdb_aliastool fails
blast
updated 6 hours ago by
GenoMax
151k • written 2 days ago by
etienne
• 0
2
votes
2
replies
248
views
Why is this interaction result not significant in DESeq2
DEG
DE
interaction
DESeq2
RNA-seq
updated 2 days ago by
yura.grabovska
▴ 760 • written 3 days ago by
Guillermo
▴ 10
0
votes
0
replies
113
views
Combining scRNA-seq datasets that have been processed differently
immunology
Seurat
2 days ago by
S
• 0
6
votes
8
replies
12k
views
7 follow
WGCNA package in R: dendogram plot error
wgcna
R
updated 2 days ago by
GenoMax
151k • written 8.3 years ago by
zyr123
▴ 40
1
vote
1
reply
138
views
Problem with galaxy's Maxquant
Proteomics
Maxquant
Galaxy
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Chris K
▴ 10
0
votes
0
replies
112
views
Workflow for DE after high-resolution CibersortX deconvolution
CibersortX
Deconvolution
2 days ago by
Aspire
▴ 380
0
votes
0
replies
116
views
Is there any way to treat antibody titers as continuous data for microbiome analysis?
antibody-titers
immunology
microbiome
2 days ago by
nmarin
• 0
0
votes
0
replies
579
views
How to analyze transcriptional trends over time from multiple RNA-seq datasets with similar but not identical conditions?
pathway-analysis
rnaseq
differential-expression
meta-analysis
time-series
2 days ago by
enee
▴ 20
0
votes
0
replies
109
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
2 days ago by
ecSeq Bioinformatics
▴ 20
53
votes
11
replies
49k
views
When and why is bwa aln better then bwa mem?
aln
comparison
bwa
mem
2 days ago by
dariober
15k
0
votes
1
reply
148
views
How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
aneuploid
updated 5 hours ago by
dthorbur
★ 2.9k • written 2 days ago by
analyst
▴ 60
0
votes
2
replies
190
views
False positives annotation of Augustus?
Augustus
training
updated 2 days ago by
lieven.sterck
15k • written 2 days ago by
Joseph
• 0
1
vote
2
replies
286
views
Mapping SNPs to genes
biomart
SNP
ensembl
r
gene
2 days ago by
Nigussie
• 0
0
votes
2
replies
189
views
Rockhopper Reference Genome Error
Rockhopper
2 days ago by
ATS
• 0
0
votes
0
replies
128
views
What can cause Faststructure to produce really high K clusters as optimal (e.g. 12 - 14)
SNP
vcf
population
2 days ago by
Drew
▴ 10
0
votes
7
replies
1.1k
views
Trouble finding datasets
GEO
SRA
updated 2 days ago by
ehaag
▴ 20 • written 18 months ago by
SHXVRR
▴ 20
4
votes
2
replies
998
views
Imputation server failing to see samples in VCF files
imputation
VCF
updated 3 days ago by
Andresa Raquel Capodifoglio
• 0 • written 19 months ago by
Ben
▴ 10
0
votes
3
replies
232
views
Read Mapping of Reads to Reference Genome Shows Extreme Bias
mapping
read
bwa-mem
coverage
updated 2 days ago by
Michael
55k • written 3 days ago by
Lawrence
• 0
0
votes
0
replies
137
views
News:
Introduction to Python for Biologists (IPYB01)
Python
updated 3 days ago by
GenoMax
151k • written 3 days ago by
oliverhooker
▴ 110
0
votes
0
replies
137
views
News:
Machine Learning using Python (MLUP01)
Python
updated 3 days ago by
GenoMax
151k • written 3 days ago by
oliverhooker
▴ 110
2
votes
2
replies
224
views
Interpreting a vcf file
variant
vcf
updated 1 day ago by
cmdcolin
★ 4.2k • written 3 days ago by
ramiro.barrantes
▴ 20
3
votes
0
replies
169
views
Herald:
The Biostar Herald for Tuesday, April 29, 2025
herald
3 days ago by
Biostar
3.5k
5
votes
2
replies
331
views
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG
GSEA
single-cell
pseudobulk
11 hours ago by
txema.heredia
▴ 210
6
votes
8
replies
2.6k
views
7 follow
Cluster annotation in single cell
Single-cell
updated 3 days ago by
Ethan
• 0 • written 20 months ago by
synat.keam
▴ 100
3
votes
6
replies
6.6k
views
Manual annotation of cell types in single cell RNA-seq
Seurat
single_cell
annotation
updated 3 days ago by
Ethan
• 0 • written 3.7 years ago by
Gene_MMP8
▴ 240
3
votes
7
replies
398
views
Clustal Omega stand alone versus website percent identity matrix
clustal
MSA
identity
percent
2 days ago by
sorrymouse
▴ 120
0
votes
1
reply
236
views
PCA vs sparse PCA : differences in results
ML
updated 3 days ago by
Ram
45k • written 4 days ago by
Ariadna
▴ 20
121,096 results • Page
1 of 2422
Recent Votes
Answer: Deduplication rate of shotgun metagenomes using fastqc
Remove short sequences with length < 50% from a multi-fasta file
Answer: Remove short sequences with length < 50% from a multi-fasta file
Answer: Remove short sequences with length < 50% from a multi-fasta file
Why Are There No Proteomics Questions In Biostar?
Answer: Deduplication rate of shotgun metagenomes using fastqc
Answer: Lucidea Array Spotter - Question about machinery
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Recent Replies
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
Bastien Hervé
6.2k
> Are scater::runPCA's underlying assumptions/method incompatible with SCT transformation? Potentially. Could you try doing a dummy test w…
Comment: What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
by
GenoMax
151k
While we wait for answers in this specific case, it may be best to post your question at JASPAR's google group site: https://groups.google.…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Mensur Dlakic
★ 29k
I don't think anyone can help you when the only feedback you provide is "there are some errors occurring." If I told you that I tried to bu…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Nikesh
• 0
Hi t tried to work with this, but there are some errors occurring, Do you have code or any source material to work on this ? @mensur
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
txema.heredia
▴ 210
Thanks for your input. Yes, the cell types are closely related. Both cell types have already been identified in multiple single cell paper…
Comment: How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
by
dthorbur
★ 2.9k
Is there any way to estimate ploidy from the supplier, or from the ancestors that established the hybrids? I would suggest making an educ…
Comment: Lucidea Array Spotter - Question about machinery
by
Taylor
• 0
Thank you so much!
Answer: Lucidea Array Spotter - Question about machinery
by
GenoMax
151k
This is a microarray spotting/printing machine that was likely used to "print" oligos (complementary to specific genes etc) on array substr…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
GenoMax
151k
> ERROR ~ No such file or directory: /home/gigiux/Downloads/ALIGN/target_genome_file.fa Looks like the error is now with a different file.
Comment: Create local Blast database alias with blastdb_aliastool fails
by
GenoMax
151k
You can use `blastdbcmd` to retrieve data from pre-formatted databases. An example that is supposed to retrieve `gi` numbers is the command…
Comment: Deduplication rate of shotgun metagenomes using fastqc
by
vikasmh111
• 0
Thank you, will try and check.
Comment: How to generate identiy score between aligned sequences with Mauve?
by
marongiu.luigi
▴ 740
Thank you, I tried but this time I got: ``` ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details T…
Answer: Deduplication rate of shotgun metagenomes using fastqc
by
GenoMax
151k
> Is fastqc a reliable tool for estimation of duplication of reads in metagenomes? While `FastQC` is a reliable tool because of the time/…
Answer: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
Bastien Hervé
6.2k
I would inspect the `loadings` of the PCAs rather than a strict `PC1 vs. PC1v2`. Check first if the genes driving PC1 are the same as the o…
Comment: Need help to perform survival analysis
by
Yugan Gogul Muthukumar
▴ 10
You have to state it clearly regarding what's your objective and what's your problem, if you're facing an error describe the error and ask …
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