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116,681 results • Page
1 of 2334
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Votes
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0
votes
0
replies
5
views
unable to get feature count results
count
file
error
in
feature
10 minutes ago by
Ravita
• 0
0
votes
0
replies
12
views
Subsetting and merging back Seurat Object brings different results
Seurat
10 minutes ago by
Bine
▴ 60
0
votes
0
replies
17
views
KEGG Pathways
rna-seq
r
57 minutes ago by
Sudip
• 0
4
votes
6
replies
3.7k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 57 minutes ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
17
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
58 minutes ago by
Bine
▴ 60
0
votes
1
reply
143
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
1 hour ago by
David Langenberger
11k
0
votes
0
replies
19
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
1 hour ago by
Dora
▴ 10
0
votes
0
replies
19
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 hour ago by
8armed
• 0
0
votes
1
reply
53
views
Deseq2
Deseq2
updated 2 hours ago by
Jack Tierney
▴ 360 • written 3 hours ago by
Sudip
• 0
0
votes
1
reply
93
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 2 hours ago by
Michael
54k • written 12 hours ago by
Lissa Cruz Saavedra
• 0
1
vote
3
replies
117
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 hours ago by
Lluís R.
★ 1.2k • written 4 hours ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
71
views
MA plot of shrunken fold change
MA
plot
Deseq2
3 hours ago by
Sudip
• 0
1
vote
1
reply
62
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
count
file
error
in
feature
updated 2 hours ago by
Michael
54k • written 3 hours ago by
Ravita
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
31
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
4 hours ago by
Adyasha
• 0
0
votes
0
replies
39
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
7 hours ago by
fanglujing
▴ 60
0
votes
0
replies
54
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
9 hours ago by
Jacob
• 0
0
votes
3
replies
656
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 10 hours ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
159
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 5 hours ago by
Ram
43k • written 12 hours ago by
Hamtaro
▴ 50
0
votes
1
reply
110
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 hours ago by
LChart
3.9k • written 18 hours ago by
kl
▴ 10
0
votes
1
reply
100
views
Differential Accessibility
DiffBind
updated 13 hours ago by
Ram
43k • written 14 hours ago by
Shloka
• 0
0
votes
2
replies
146
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
8 hours ago by
kim
• 0
3
votes
2
replies
277
views
Extract protein sequence
fasta
alignment
blast
1 hour ago by
anna
▴ 20
0
votes
3
replies
211
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 18 hours ago by
noodle
▴ 570 • written 1 day ago by
WUSCHEL
▴ 750
0
votes
4
replies
214
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 15 hours ago by
Wayne
★ 2.0k • written 21 hours ago by
Mariana
▴ 10
0
votes
1
reply
91
views
metagenomic virome quality assessment
viromics
metagenomics
updated 18 hours ago by
Ram
43k • written 21 hours ago by
Petchimuthu
• 0
3
votes
7
replies
219
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
17 hours ago by
salias
• 0
0
votes
0
replies
60
views
Using limma in methylation EM-seq?
EM-seq
methylation
19 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
503
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
18 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
69
views
Synteny analysis
bacterial
synteny
genome
updated 19 hours ago by
GenoMax
141k • written 19 hours ago by
Namil
• 0
0
votes
4
replies
143
views
Genbank File Format
gbkformat
2 hours ago by
alenew.am
• 0
0
votes
5
replies
322
views
How should I make kallisto indexes?
kallisto
updated 17 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
138
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
20 hours ago by
SSSJec
• 0
0
votes
3
replies
161
views
Software to separate reads from different individuals
software
development
nanopore
updated 16 hours ago by
GenoMax
141k • written 20 hours ago by
njornet
▴ 20
0
votes
0
replies
62
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
20 hours ago by
David
• 0
4
votes
5
replies
227
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 21 hours ago by
dsull
★ 5.9k • written 1 day ago by
Kazo
▴ 10
0
votes
2
replies
127
views
How to update R on ubuntu
installation
update
R
apt-get
20 hours ago by
Bosberg
▴ 50
4
votes
0
replies
96
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
22 hours ago by
Biostar
2.7k
0
votes
1
reply
106
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
Ruqaiya
• 0
0
votes
1
reply
256
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 23 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
79
views
LEfSe
LEfSe
23 hours ago by
benkosta
• 0
0
votes
0
replies
67
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
21 hours ago by
Sara
▴ 30
1
vote
4
replies
340
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
21 hours ago by
hagl
▴ 10
0
votes
1
reply
111
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 1 day ago by
matteo.levorato
• 0
0
votes
2
replies
119
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
1 day ago by
Lluís R.
★ 1.2k
0
votes
1
reply
116
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
DOBI
• 0
0
votes
0
replies
83
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
1 day ago by
atharvakarkare14
▴ 10
5
votes
16
replies
585
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
1 day ago by
Ruqaiya
• 0
0
votes
2
replies
165
views
What should I consider as FASTA for dataset?
PDB
FASTA
14 hours ago by
Nafi
• 0
35
votes
24
replies
1.6k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
i.sudbery
19k • written 2 days ago by
noodle
▴ 570
116,681 results • Page
1 of 2334
Recent Votes
Answer: Single-stranded RNA-seq: strandedness of samples
Comment: NGS forensics: how to know if data is fabricated
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
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ATpoint
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Recent Replies
Answer: Taking the difference of two VCFs (or removing singletons)
by
Andres
▴ 20
I know this is an old question but when searching for filtering out singletons(and doubletons too) i found this post in the first results. …
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
In which case, I'd definately look at the distribution of read lengths, post trimming, and see if there is a discontinuity in the distribut…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
I would note that even on a good, polyA selected, RNA-seq run, I would only expect 60-75% of mapped reads to map to protein coding exons.
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
:: FINAL CALL :: 8th Berlin Summer School in NGS Data Analysis 2024 - Only a few last places available
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
Answer: Deseq2
by
Jack Tierney
▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format
by
alenew.am
• 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format
by
alenew.am
• 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
by
Michael
54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
by
Lluís R.
★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Michael
54k
You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
Comment: MA plot of shrunken fold change
by
Sudip
• 0
Thank you.
Comment: MA plot of shrunken fold change
by
ATpoint
82k
You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
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