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121,192 results • Page
1 of 2424
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Votes
Replies
3
votes
4
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891
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Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq
NGS
pipeline
INDELs
SNVs
2 hours ago by
CHOCADAPASSADAEMCHOQ
• 0
0
votes
0
replies
64
views
How important are allele fractions when calling variants?
GATK
bacteria
BCFTools
6 hours ago by
andean
• 0
0
votes
0
replies
63
views
Job:
Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
generativeAI
bioinformatics
cancer_detection
nucleosomes
8 hours ago by
Jakob Skou
• 0
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 19 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
2
replies
1.5k
views
Analysing Problem Seen In MEGA X
Alignment
MEGAX
Muscle
updated 14 hours ago by
humarafique.1234
• 0 • written 3.5 years ago by
ankurhalder116
• 0
0
votes
0
replies
116
views
discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
Analysis
Enrichment
updated 16 hours ago by
Philip
• 0 • written 1 day ago by
ricardo
• 0
0
votes
0
replies
87
views
DESeq2 outliers-should I be concerned?
deseq2
1 day ago by
bioinfo
▴ 150
0
votes
2
replies
245
views
Trimmomatic command
STAR
RNASeq
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
rajdeepboral00
▴ 60
1
vote
1
reply
179
views
Blog:
Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
updated 1 day ago by
cmdcolin
★ 4.2k • written 2 days ago by
Novogene
▴ 510
4
votes
8
replies
893
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 1 day ago by
ATpoint
88k • written 6 weeks ago by
harsh
▴ 20
4
votes
2
replies
208
views
Forum:
Pie Charts: to use or not to use
pie-chart
graphs
updated 1 day ago by
Joe
22k • written 1 day ago by
littlebioinformatician
• 0
1
vote
1
reply
150
views
Minimum Number of Cells for Downstream Analysis after subsetting a particular cell type (scRNAseq)?
cell
single
updated 1 day ago by
ATpoint
88k • written 1 day ago by
Tundup
▴ 10
0
votes
3
replies
322
views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif
NCBI_genome_database
Acinetobacter_guillouiae
Nitrogenase
Nitrogen_fixation
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Nafi
• 0
0
votes
1
reply
154
views
Target prediction
protien
prediction
Target
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
Samprath
• 0
6
votes
12
replies
710
views
Heatmap of a transformed deseq object with pheatmap
deseq2
pheatmap
2 days ago by
caroline.zanchi
• 0
0
votes
0
replies
111
views
CNVkit CNVs call with threshold issues
CNVkit
threshold_log2
Somatic_variant
2 days ago by
AIMAR
• 0
2
votes
2
replies
248
views
PRS result interpretation
risk
score
PRS
interpretation
polygenic
2 days ago by
trkfs
▴ 10
1
vote
0
replies
123
views
Several errors in DROP Workflow
DROP
aberrantSplicing
FRASER
RNAseq
1 day ago by
n_navy
▴ 10
2
votes
1
reply
196
views
More rare variants than common variants
PLINK
GWAS
updated 2 days ago by
LChart
4.9k • written 2 days ago by
RT
▴ 20
1
vote
1
reply
240
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated 3 days ago by
Jordan M Eizenga
▴ 740 • written 4 days ago by
gulin
• 0
0
votes
0
replies
157
views
Job:
Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD
learning
bioinformatics
deep
genomics
3 days ago by
bjdaigle
▴ 10
5
votes
4
replies
543
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 3 days ago by
LChart
4.9k • written 8 days ago by
sardius
• 0
2
votes
1
reply
222
views
Regressing variables for finding Differentially expressed genes
batcheffect
seurat
bias
scRNASeq
updated 3 days ago by
Bastien Hervé
6.3k • written 3 days ago by
AB
▴ 390
0
votes
0
replies
197
views
Job:
Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany
e14
3 days ago by
elsalatino
• 0
2
votes
1
reply
243
views
GSEA and Cytoscape Enrichment maps
Cytoscape
RNA-seq
GSEA
updated 3 days ago by
Bastien Hervé
6.3k • written 4 days ago by
kdca
• 0
1
vote
1
reply
275
views
Alternatives to WGCNA
WGCNA
updated 3 days ago by
LChart
4.9k • written 4 days ago by
Poorvi
▴ 10
8
votes
4
replies
430
views
RNA-seq analysis
Htseq-count
HiSat2
featurecounts
STAR
updated 2 days ago by
Gordon Smyth
★ 8.1k • written 4 days ago by
SEJAL
• 0
2
votes
2
replies
1.2k
views
Liquid Biopsy datasets
RNA-Seq
next-gen
liquid biopsy
miRNA
cDNA
updated 4 days ago by
ehaag
▴ 80 • written 4.7 years ago by
pacocp
• 0
1
vote
4
replies
1.1k
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 4 days ago by
ehaag
▴ 80 • written 10 months ago by
jimmysibandah
• 0
4
votes
3
replies
1.1k
views
Metagenomics mock datasets
metagenomics
updated 4 days ago by
ehaag
▴ 80 • written 16 months ago by
enuhblaise
• 0
3
votes
0
replies
215
views
News:
NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics
NCBI
codeathon
3 days ago by
MirianT_NCBI
▴ 800
1
vote
1
reply
246
views
Using structure prediction approaches to predict interaction between two proteins
protein
prediction
structure
updated 4 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
Daniel
▴ 30
3
votes
3
replies
314
views
How to visualize Combat-seq corrected counts
batch-correction
combat-seq
1 day ago by
ybw8gh
• 0
3
votes
6
replies
411
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
3 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
275
views
Umbrella pathways in KEGG
KEGG
R
updated 4 days ago by
Arup Ghosh
3.3k • written 5 days ago by
Arindam Ghosh
▴ 540
0
votes
2
replies
234
views
Peptide protein dynamics
Pepdide
updated 4 days ago by
lieven.sterck
15k • written 4 days ago by
venkatramananspd
• 0
2
votes
4
replies
354
views
variant calling chromosome-wise from WGS data
wgs
updated 3 days ago by
GenoMax
151k • written 4 days ago by
analyst
▴ 60
5
votes
5
replies
351
views
Design matrix with uneven patient representation across stages
RNA-seq
design-matrix
limma
4 days ago by
Lucas
• 0
1
vote
2
replies
289
views
Forum:
The best LLM or any tool to generate legal regex expression string for specific usage?
regex
awk
sed
commands
linux
updated 4 days ago by
GenoMax
151k • written 4 days ago by
JustinZhang
▴ 140
3
votes
6
replies
2.2k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 4 days ago by
Arup Ghosh
3.3k • written 14 months ago by
michael.flower.14
▴ 200
0
votes
1
reply
229
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
updated 3 days ago by
lieven.sterck
15k • written 4 days ago by
debitboro
▴ 270
6
votes
10
replies
2.8k
views
Minimap2 error in Flye de novo assembly
Flye
Minimap2
4 days ago by
Nilo
▴ 20
0
votes
0
replies
252
views
How to find hormone related proteins from a list of gene/proteins
R
updated 4 days ago by
Ram
45k • written 4 days ago by
WUSCHEL
▴ 860
0
votes
0
replies
264
views
mtDNA variants from WGS data
mitogenome
WGS
updated 4 days ago by
Ram
45k • written 4 days ago by
wonde2000
• 0
0
votes
1
reply
246
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF
LiftoverVcf
Merge
updated 5 days ago by
Giulio Genovese
▴ 630 • written 5 days ago by
JourneyToAbyss
▴ 240
0
votes
0
replies
203
views
Writing genepop from genind
R
genepop
genind
graph4lg
stacks
5 days ago by
eaabbott0
• 0
3
votes
4
replies
2.1k
views
Remove all entries with duplicate names from fastq file?
fastq
illumina
duplicate
updated 5 days ago by
Charles-Alexandre Roy
▴ 50 • written 3.9 years ago by
wormball
▴ 10
1
vote
1
reply
249
views
Copy Number Variants with CNVKit
CVNs
Somatic_variant
Recommendations
CNVKit
updated 5 days ago by
GenoMax
151k • written 5 days ago by
AIMAR
• 0
0
votes
0
replies
208
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
5 days ago by
aj
• 0
0
votes
0
replies
210
views
TEtranscripts analysis
TEtranscripts
5 days ago by
frarodmar17
• 0
121,192 results • Page
1 of 2424
Recent Votes
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
Several errors in DROP Workflow
Single probe id for multiple genes in Microarray
Single probe id for multiple genes in Microarray
C: I can not run bcftools stats (help)
Answer: Minimap2 error in Flye de novo assembly
Answer: How to visualize Combat-seq corrected counts
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Recent Replies
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
CHOCADAPASSADAEMCHOQ
• 0
Thank you so much!! So kind!
Comment: Analysing Problem Seen In MEGA X
by
humarafique.1234
• 0
I'm also facing the same issue. Have you been able to find a way to fix it?
Comment: How to visualize Combat-seq corrected counts
by
ybw8gh
• 0
Sorry, I accidentally used ComBat! ComBat-seq did not produce negative counts. Thanks for all the help!
Answer: Trimmomatic command
by
swbarnes2
14k
Keep in mind for RNASeq 1) if the library was done properly, it's very unlikely you have many fragments shorter than your read length. …
Comment: Setaria Pan-Genome Variation: Unraveling the Story of Domestication
by
cmdcolin
★ 4.2k
>de novo assembled 110 reference-grade genomes for cultivated Setaria accessions this type of routine de novo assembly of genomes is aweso…
Comment: Facing issue with output of nextflow pipeline
by
ATpoint
88k
It looks hacky. Maybe it "works" but should not be taken as inspiration I guess. Are you sure output could be redicted to other processed l…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
GenoMax
151k
Have you considered the possibility that if no strains of Acinetobacter guillouiae available in NCBI show presence of nitrogen fixing genes…
Answer: Facing issue with output of nextflow pipeline
by
neng
▴ 50
This is a common issue that many learners encounter when working with Nextflow output management. 1. Use publishDir("${params.outdir}/..…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Nafi
• 0
Yes, I have tested all of them. I guess NCBI does not have this particular strain.
Answer: Pie Charts: to use or not to use
by
Joe
22k
As with any visualisation method, there is a time and a place for them. They are often misused, or used when a different method would be be…
Answer: Pie Charts: to use or not to use
by
Bastien Hervé
6.3k
Your first paragraph is answering the latter and as said in the second paragraph, one cannot force people not to use it. It is like RPKM/F…
Comment: Target prediction
by
dthorbur
★ 3.0k
I'm unfamiliar with the representation of phytochemicals in either database, so can't answer for certain, but generally I would say both da…
Answer: Minimum Number of Cells for Downstream Analysis after subsetting a particular ce
by
ATpoint
88k
There is no answer to this. Some people will say 10, other 3, others 500. Generally, since single-cell is noisy and has dropouts, even for …
Answer: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Mensur Dlakic
★ 29k
The specific strain described in that paper (*Acinetobacter guillouiae* EU-B2RT.R1) doesn't seem to be available in NCBI. It could be as si…
Comment: Heatmap of a transformed deseq object with pheatmap
by
GenoMax
151k
Please use `ADD REPLY/ADD COMMENT` when responding to existing posts. `ADD ANSWER` is only for new answers to original question.
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