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120,691 results • Page
1 of 2414
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0
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28
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illumina: Adapter Confusion
ILLUMINA
ADAPTER
16 minutes ago by
lingjun meng
▴ 20
0
votes
0
replies
18
views
Identifying primer sequences from raw FASTQ files
primers
1 hour ago by
Chandini
• 0
1
vote
6
replies
1.2k
views
HTSlib threads when ingesting large bgzipped FASTA
htslib
samtools
bgzip
c
updated 7 hours ago by
Erik Garrison
★ 2.4k • written 20 months ago by
Oleksii
• 0
834
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
3
votes
3
replies
161
views
question for dowloading Protein fasta sequence by edirect using while
edirect
updated 7 hours ago by
vkkodali_ncbi
★ 3.8k • written 1 day ago by
诗友
• 0
1
vote
1
reply
551
views
Validate RNAseq Models in Microarray Data?
microarray
rnaseq
coxlasso
fpkm
updated 9 hours ago by
nuorain
▴ 40 • written 2.7 years ago by
vitor
▴ 130
0
votes
0
replies
52
views
Restrict anlaysis of WGS VCF file to Refseq Select using snpeff
refseq
vcf
wgs
11 hours ago by
Gabriel
• 0
2
votes
1
reply
85
views
Why do RNAseq reads align to non-gene regions of the bacterial genome?
RNAseq
transcription
updated 12 hours ago by
Mensur Dlakic
★ 29k • written 12 hours ago by
Texx
▴ 30
0
votes
0
replies
57
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
14 hours ago by
s.may-wilson
▴ 50
0
votes
2
replies
118
views
Novel genes in model organisms
homologue
genome
gene
17 hours ago by
zizigolu
★ 4.3k
0
votes
1
reply
129
views
Understanding sctransform
sctransform
Seurat
updated 18 hours ago by
Bastien Hervé
6.1k • written 18 hours ago by
Deepak Tanwar
★ 4.2k
1
vote
1
reply
150
views
Subset reads based on Phred-score ranges
phred
sequencing
ngs
updated 17 hours ago by
GenoMax
149k • written 21 hours ago by
Mark
▴ 30
4
votes
1
reply
140
views
Reasoning - Why is it invalid to compare ratios of TPMs?
RNAseq
analysis
expression
normalization
differential
TPM
batch
effect
updated 22 hours ago by
ATpoint
87k • written 22 hours ago by
VTh
• 0
2
votes
2
replies
206
views
DEGs Analysis For a Microarray Data that has one biological replicates per cell line in each condition
Analysis
DEGs
Microarray
15 hours ago by
mete.han.celebi
• 0
1
vote
6
replies
253
views
The soapdenovo2 genome assembly is highly fragmented - learning genome assembly with public data
Gene
soapdenovo2
assembly
updated 15 hours ago by
lieven.sterck
15k • written 1 day ago by
JieQY
• 0
0
votes
1
reply
100
views
Cytoscape COLOUR EDGES
Reulatory
Cytoscape
Networks
updated 4 hours ago by
Scooter
▴ 280 • written 1 day ago by
SKY
▴ 60
3
votes
3
replies
448
views
VCF filtering with Allele Balance (AB) using FilterVcf (Picard)
Allele-Balance
FilterVcf
Picard
GATK
updated 1 day ago by
GokalpC
▴ 160 • written 13 days ago by
Eduardo
▴ 20
1
vote
3
replies
450
views
Haplotype analysis
founder
haplotype-analysis
updated 1 day ago by
GokalpC
▴ 160 • written 22 days ago by
disha3786
• 0
3
votes
4
replies
273
views
Indica rice genome and annotation files
RNASeq
updated 1 day ago by
ChanderKant (CK) Chaudhary
▴ 10 • written 2 days ago by
chandimaa
• 0
2
votes
6
replies
311
views
Question: Making primers for cloning and transfection
transfection
cloning
primer
PCR
gene
updated 18 hours ago by
jared.andrews07
★ 18k • written 1 day ago by
Lu Adr
• 0
0
votes
0
replies
103
views
Help with the interpretation of Silhouette width averaging
clustering
kmeans
cluster
silhouettemethod
1 day ago by
Maria Jose
• 0
0
votes
1
reply
163
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Cancer
Oncology
Tenure-earning
Faculty
Bioinformatics
updated 1 day ago by
GenoMax
149k • written 1 day ago by
maritza.garcia-saavedra
• 0
0
votes
1
reply
150
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Oncology
Faculty
Leadership
updated 1 day ago by
GenoMax
149k • written 1 day ago by
maritza.garcia-saavedra
• 0
35
votes
14
replies
1.2k
views
12 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
written 6 weeks ago by
sviatoslav.kendall
▴ 960
0
votes
0
replies
148
views
Tutorial:
CC-By 4.0 Project (unpublished papers and data) release on OSF - Discoveries of 2nd/3rd order gene combinations for static/time series data in cell/…
MachineLearning
GeneCombination
CellSignaling
SensitivityAnalysis
9 hours ago by
sinha.shriprakash
▴ 20
1
vote
1
reply
146
views
Pre-Alignment process
read_depth_measure
updated 1 day ago by
GenoMax
149k • written 1 day ago by
AIMAR
• 0
0
votes
0
replies
115
views
Differential methylation analysis using Dorado
dorado
m6A
DRS
nanopore
1 day ago by
baibhu1234
▴ 20
0
votes
0
replies
107
views
Annotate Phylogentic Tree with classes
python
tree
phylogenetic
analysis
1 day ago by
BIANCA
• 0
1
vote
1
reply
153
views
Is it possible for genomic DNA to be sequenced in a modern RNA-seq protocol?
transcriptome
genome
RNA-seq
updated 1 day ago by
GenoMax
149k • written 1 day ago by
predeus
★ 2.1k
1
vote
3
replies
221
views
Picard gives empty value for HS_LIBRARY_SIZE when running CollectHsMetrics
sequencing
library
picard
22 hours ago by
Bertalan_Takacs
▴ 120
1
vote
2
replies
159
views
single cell compositional analysis - how adjusting for covariates (age)
compositional-analysis
RNA-seq
single-cell
10 minutes ago by
Francesco
▴ 20
0
votes
1
reply
148
views
Differential Expression Analysis of scRNA seq data with Pseudobulking
edgeR
scrnaseq
pseudobulking
updated 1 day ago by
ATpoint
87k • written 1 day ago by
Sophia
• 0
9
votes
20
replies
7.4k
views
11 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 14 hours ago by
tony_s
▴ 10 • written 6 months ago by
Martina
• 0
0
votes
0
replies
109
views
News:
Last Two Spots Available – R/Bioconductor for Mass Spectrometry & Proteomics
Proteomics
Bioconductor
Mass-Spectrometry
R
updated 1 day ago by
Ram
45k • written 2 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
104
views
News:
Last-Minute Open Spots for Our RNA-Seq Workshops!
single-cell
transcriptomics
scRNAseq
RNAseq
updated 1 day ago by
Ram
45k • written 2 days ago by
ecSeq Bioinformatics
▴ 10
2
votes
2
replies
322
views
advice on rooting a tree in R
R
tree
ggtree
phylo
22 hours ago by
Matteo Ungaro
▴ 110
0
votes
1
reply
198
views
Beagle removed many sites in the target dataset after imputation
genotype
beagle
imputation
2 days ago by
LCG
• 0
0
votes
0
replies
95
views
Blog:
Novogene Single-cell and Spatial Multi-omics Case Study: Application in Immunosenescence
Single-cell
2 days ago by
Novogene
▴ 500
0
votes
2
replies
709
views
ArchR error Error in grid.Call.graphics(C_downvppath, name$path, name$name, strict): Viewport 'Norm. Enrichment -log10(P-adj) [0-Max]_heatmap_body_1_…
ArchR
2 days ago by
Bioinformatics_16
• 0
3
votes
5
replies
6.1k
views
normalization to "housekeeping" genes of RNAseq data vs qPCR result
qPCR
RNAseq
updated 2 days ago by
Conor
• 0 • written 3.6 years ago by
cwwong13
▴ 40
0
votes
12
replies
672
views
MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genome
reference-genome
updated 2 days ago by
GenoMax
149k • written 4 days ago by
offset
• 0
2
votes
8
replies
2.7k
views
6 follow
Normalizing TCR data
Analysis
updated 2 days ago by
apontel
• 0 • written 6.1 years ago by
ruchitkpanchal
• 0
0
votes
1
reply
211
views
Alternative normalization strategy for RNA-seq data with global downregulation
DESeq2
RNA-seq
GeneExpression
Normalization
miRNA
updated 1 day ago by
ATpoint
87k • written 2 days ago by
Nicolas
• 0
1
vote
2
replies
214
views
Extract Fungal mRNA reda from RNASeq Sample
rnaseq
rna
fungus
bbsplit.sh
transcriptomics
2 days ago by
SomeOne
▴ 170
0
votes
0
replies
142
views
cNMF missing spectra iterations - what am I doing wrong?
cNMF
python
single-cell
2 days ago by
yura.grabovska
▴ 730
0
votes
0
replies
144
views
Repeated sequences
Repetitive
sequences
2 days ago by
frarodmar17
• 0
1
vote
7
replies
475
views
Best way to assess relatedness of eukaryotic organisms from sequencing reads?
phylogenomics
phylogenetics
ngs
kmer
sequencing
updated 3 days ago by
colindaven
7.3k • written 6 days ago by
Mark
▴ 30
1
vote
0
replies
160
views
Potential Contamination in ARG Metagenomic Analysis – How to Filter Out Reads?
metagenomics
ARG
3 days ago by
JH
▴ 10
1
vote
2
replies
306
views
Negative coverage depths when running jgi_summarize_bam_contig_depths (Metabat2)
assembly
metagenome
Metabat
3 days ago by
amir.rakhimov.b
• 0
0
votes
0
replies
171
views
How to interpret this RNA-seq multi-peak distribution density plot?
rna-seq
distribution
3 days ago by
Omar
• 0
120,691 results • Page
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A: Transcript differential exprs analysis using Kallisto not significant
Answer: question for dowloading Protein fasta sequence by edirect using while
Comment: single cell compositional analysis - how adjusting for covariates (age)
A: What is the difference between deferentially expressed genes and deferentially
What is the difference between deferentially expressed genes and deferentially expressed transcripts?
A: How to add rsIDs to VCF?
Comment: DEGs Analysis For a Microarray Data that has one biological replicates per cell
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Comment: single cell compositional analysis - how adjusting for covariates (age)
by
Francesco
▴ 20
thank you, much appreciated
Answer: illumina: Adapter Confusion
by
lingjun meng
▴ 20
Cant edit answer because of the great fire wall
Comment: Cytoscape COLOUR EDGES
by
Scooter
▴ 280
Can you provide a little more information? Exactly what are you having problems with? -- scooter
Comment: question for dowloading Protein fasta sequence by edirect using while
by
vkkodali_ncbi
★ 3.8k
Two nuances -- 1. When you know that the query string is a gene symbol, it's better to search nuccore database as `-query 'LOC121999999[G…
Answer: HTSlib threads when ingesting large bgzipped FASTA
by
Erik Garrison
★ 2.4k
I've implemented a reentrant/thread-safe single header extension to htslib that allows efficient multithreaded use of a single static fai/b…
Answer: question for dowloading Protein fasta sequence by edirect using while
by
vkkodali_ncbi
★ 3.8k
> the question is the script just run using the first line LOC8030992 and stop. You need to use a `</dev/null` with your while loop. See…
Comment: Validate RNAseq Models in Microarray Data?
by
nuorain
▴ 40
I have the same question. Why is there no comment for this question.
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
by
Mensur Dlakic
★ 29k
> I'm wondering whether the real reason is actually that the RNA polymerase during the transcription doesn't stop immediately at the end of…
Comment: Troubleshooting a REGENIE sex-stratified GWAS
by
s.may-wilson
▴ 50
Apologies for never getting back to this. Unfortunately in the end we actually just abandoned this particular GWAS. In fact our results for…
Comment: The soapdenovo2 genome assembly is highly fragmented - learning genome assembly
by
lieven.sterck
15k
OK, data is on the low end for ATH but should still get you better result than you get ... also the Kmer analysis result is a bit funky, w…
Comment: DEGs Analysis For a Microarray Data that has one biological replicates per cell
by
mete.han.celebi
• 0
Thank you very much for your valuable reply! I got very nice DEGs for TNFa and IFNg groups which totally makes sense. However, for IFNa gro…
Comment: The soapdenovo2 genome assembly is highly fragmented
by
colindaven
7.3k
Use current long read data from ONT or Pacbio and, like you are doing, a small-ish genome like Arabidopsis. I would use illumina data more …
Comment: Novel genes in model organisms
by
zizigolu
★ 4.3k
The goal is to translate these findings to searching for novel genes/pathways in humans/patients. Although I can not think how
Comment: Novel genes in model organisms
by
dthorbur
★ 2.9k
Blast with parameters set to identify distant homologs? But if they are truly novel genes, what are you getting out of this search for most…
Answer: question for dowloading Protein fasta sequence by edirect using while
by
GenoMax
149k
> LOC121835630,LOC121835700,LOC121999999 are ncRNA. Since these are ncRNA they are not going to be found in the `protein` database. You wi…
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