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1,105 results • Page
1 of 23
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0
votes
1
reply
5
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated just now by
GenoMax
141k • written 8 minutes ago by
Riccardo
▴ 10
0
votes
0
replies
13
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
GATK
somatic_variants
variant_calling
22 minutes ago by
Alexandros
• 0
0
votes
0
replies
7
views
unable to get feature count results
count
file
error
in
feature
50 minutes ago by
Ravita
• 0
0
votes
0
replies
15
views
Subsetting and merging back Seurat Object brings different results
Seurat
57 minutes ago by
Bine
▴ 60
0
votes
0
replies
19
views
KEGG Pathways
rna-seq
r
1 hour 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 1 hour ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
19
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 hour ago by
Bine
▴ 60
0
votes
1
reply
151
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
2 hours ago by
David Langenberger
11k
0
votes
0
replies
25
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
2 hours ago by
Dora
▴ 10
0
votes
0
replies
25
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 hours ago by
8armed
• 0
0
votes
1
reply
64
views
Deseq2
Deseq2
updated 3 hours ago by
Jack Tierney
▴ 360 • written 4 hours ago by
Sudip
• 0
0
votes
1
reply
96
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 3 hours ago by
Michael
54k • written 13 hours ago by
Lissa Cruz Saavedra
• 0
1
vote
3
replies
123
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 3 hours ago by
Lluís R.
★ 1.2k • written 5 hours ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
75
views
MA plot of shrunken fold change
MA
plot
Deseq2
3 hours ago by
Sudip
• 0
1
vote
1
reply
67
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
count
file
error
in
feature
updated 3 hours ago by
Michael
54k • written 4 hours ago by
Ravita
• 0
0
votes
0
replies
32
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
4 hours ago by
Adyasha
• 0
0
votes
0
replies
40
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
8 hours ago by
fanglujing
▴ 60
0
votes
0
replies
55
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
10 hours ago by
Jacob
• 0
0
votes
3
replies
657
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 11 hours ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
160
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 6 hours ago by
Ram
43k • written 13 hours ago by
Hamtaro
▴ 50
0
votes
1
reply
111
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 14 hours ago by
LChart
3.9k • written 18 hours ago by
kl
▴ 10
0
votes
1
reply
101
views
Differential Accessibility
DiffBind
updated 14 hours ago by
Ram
43k • written 14 hours ago by
Shloka
• 0
0
votes
3
replies
148
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated just now by
GenoMax
141k • written 15 hours ago by
kim
• 0
3
votes
2
replies
278
views
Extract protein sequence
fasta
alignment
blast
2 hours ago by
anna
▴ 20
0
votes
3
replies
212
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 19 hours ago by
noodle
▴ 570 • written 1 day ago by
WUSCHEL
▴ 750
0
votes
4
replies
215
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 16 hours ago by
Wayne
★ 2.0k • written 22 hours ago by
Mariana
▴ 10
0
votes
1
reply
92
views
metagenomic virome quality assessment
viromics
metagenomics
updated 18 hours ago by
Ram
43k • written 22 hours ago by
Petchimuthu
• 0
3
votes
7
replies
220
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
18 hours ago by
salias
• 0
0
votes
0
replies
62
views
Using limma in methylation EM-seq?
EM-seq
methylation
19 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
504
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
19 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
70
views
Synteny analysis
bacterial
synteny
genome
updated 20 hours ago by
GenoMax
141k • written 20 hours ago by
Namil
• 0
0
votes
4
replies
150
views
Genbank File Format
gbkformat
3 hours ago by
alenew.am
• 0
0
votes
5
replies
323
views
How should I make kallisto indexes?
kallisto
updated 18 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
139
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
163
views
Software to separate reads from different individuals
software
development
nanopore
updated 16 hours ago by
GenoMax
141k • written 21 hours ago by
njornet
▴ 20
0
votes
0
replies
63
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
21 hours ago by
David
• 0
4
votes
5
replies
228
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
128
views
How to update R on ubuntu
installation
update
R
apt-get
21 hours ago by
Bosberg
▴ 50
4
votes
0
replies
97
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
23 hours ago by
Biostar
2.7k
0
votes
1
reply
107
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
Ruqaiya
• 0
0
votes
1
reply
257
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
80
views
LEfSe
LEfSe
23 hours ago by
benkosta
• 0
0
votes
0
replies
68
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
22 hours ago by
Sara
▴ 30
1
vote
4
replies
341
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
21 hours ago by
hagl
▴ 10
0
votes
1
reply
113
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
122
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
117
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
84
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
587
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
1 day ago by
Ruqaiya
• 0
0
votes
2
replies
166
views
What should I consider as FASTA for dataset?
PDB
FASTA
15 hours ago by
Nafi
• 0
1,105 results • Page
1 of 23
Recent Votes
Comment: MA plot of shrunken fold change
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
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ATpoint
82k
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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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