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121,184 results • Page
1 of 2424
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0
votes
0
replies
22
views
CNVkit CNVs call with threshold issues
CNVkit
threshold_log2
Somatic_variant
2 hours ago by
AIMAR
• 0
2
votes
2
replies
93
views
PRS result interpretation
risk
score
PRS
interpretation
polygenic
14 minutes ago by
trkfs
▴ 10
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 17 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
0
replies
37
views
Several errors in DROP Workflow
DROP
aberrantSplicing
FRASER
RNAseq
2 hours ago by
n_navy
• 0
0
votes
0
replies
44
views
Blog:
Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
10 hours ago by
Novogene
▴ 500
2
votes
1
reply
108
views
More rare variants than common variants
PLINK
GWAS
updated 10 hours ago by
LChart
4.9k • written 14 hours ago by
RT
▴ 20
0
votes
1
reply
97
views
Trimmomatic command
STAR
RNASeq
Trimmomatic
updated 8 hours ago by
dthorbur
★ 3.0k • written 11 hours ago by
rajdeepboral00
▴ 60
1
vote
1
reply
156
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated 16 hours ago by
Jordan M Eizenga
▴ 740 • written 2 days ago by
gulin
• 0
2
votes
3
replies
303
views
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
updated 5 hours ago by
GenoMax
151k • written 18 hours ago by
CHOCADAPASSADAEMCHOQ
• 0
0
votes
0
replies
81
views
Job:
Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD
learning
bioinformatics
deep
genomics
21 hours ago by
bjdaigle
▴ 10
4
votes
4
replies
443
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 21 hours ago by
LChart
4.9k • written 6 days ago by
sardius
• 0
2
votes
1
reply
145
views
Regressing variables for finding Differentially expressed genes
batcheffect
seurat
bias
scRNASeq
updated 1 day ago by
Bastien Hervé
6.3k • written 1 day ago by
AB
▴ 390
0
votes
0
replies
125
views
Job:
Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany
e14
1 day ago by
elsalatino
• 0
2
votes
1
reply
166
views
GSEA and Cytoscape Enrichment maps
Cytoscape
RNA-seq
GSEA
updated 1 day ago by
Bastien Hervé
6.3k • written 1 day ago by
kdca
• 0
5
votes
10
replies
485
views
Heatmap of a transformed deseq object with pheatmap
deseq2
pheatmap
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
caroline.zanchi
• 0
1
vote
1
reply
202
views
Alternatives to WGCNA
WGCNA
updated 1 day ago by
LChart
4.9k • written 2 days ago by
Poorvi
▴ 10
5
votes
4
replies
310
views
RNA-seq analysis
Htseq-count
HiSat2
featurecounts
STAR
updated 7 hours ago by
Gordon Smyth
★ 8.0k • written 1 day ago by
SEJAL
• 0
2
votes
2
replies
1.2k
views
Liquid Biopsy datasets
RNA-Seq
next-gen
liquid biopsy
miRNA
cDNA
updated 1 day ago by
ehaag
▴ 80 • written 4.7 years ago by
pacocp
• 0
1
vote
4
replies
1.0k
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 1 day ago by
ehaag
▴ 80 • written 10 months ago by
jimmysibandah
• 0
4
votes
3
replies
992
views
Metagenomics mock datasets
metagenomics
updated 1 day ago by
ehaag
▴ 80 • written 16 months ago by
enuhblaise
• 0
2
votes
0
replies
145
views
News:
NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics
NCBI
codeathon
1 day ago by
MirianT_NCBI
▴ 790
1
vote
1
reply
178
views
Using structure prediction approaches to predict interaction between two proteins
protein
prediction
structure
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Daniel
▴ 30
0
votes
2
replies
187
views
How to visualize Combat-seq corrected counts
batch-correction
combat-seq
updated 1 day ago by
cfos4698
★ 1.1k • written 2 days ago by
ybw8gh
• 0
3
votes
6
replies
306
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
1 day ago by
1769mkc
★ 1.3k
0
votes
1
reply
208
views
Umbrella pathways in KEGG
KEGG
R
updated 2 days ago by
Arup Ghosh
3.3k • written 3 days ago by
Arindam Ghosh
▴ 540
0
votes
2
replies
166
views
Peptide protein dynamics
Pepdide
updated 2 days ago by
lieven.sterck
15k • written 2 days ago by
venkatramananspd
• 0
2
votes
4
replies
265
views
variant calling chromosome-wise from WGS data
wgs
updated 1 day ago by
GenoMax
151k • written 2 days ago by
analyst
▴ 60
5
votes
5
replies
268
views
Design matrix with uneven patient representation across stages
RNA-seq
design-matrix
limma
2 days ago by
Lucas
• 0
1
vote
2
replies
210
views
Forum:
The best LLM or any tool to generate legal regex expression string for specific usage?
regex
awk
sed
commands
linux
updated 2 days ago by
GenoMax
151k • written 2 days ago by
JustinZhang
▴ 140
3
votes
6
replies
2.1k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 2 days ago by
Arup Ghosh
3.3k • written 14 months ago by
michael.flower.14
▴ 200
0
votes
1
reply
161
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
updated 1 day ago by
lieven.sterck
15k • written 2 days ago by
debitboro
▴ 270
5
votes
10
replies
2.8k
views
Minimap2 error in Flye de novo assembly
Flye
Minimap2
2 days ago by
Nilo
▴ 10
0
votes
0
replies
163
views
How to find hormone related proteins from a list of gene/proteins
R
updated 1 day ago by
Ram
45k • written 2 days ago by
WUSCHEL
▴ 860
0
votes
0
replies
174
views
mtDNA variants from WGS data
mitogenome
WGS
updated 1 day ago by
Ram
45k • written 2 days ago by
wonde2000
• 0
0
votes
1
reply
177
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF
LiftoverVcf
Merge
updated 2 days ago by
Giulio Genovese
▴ 630 • written 2 days ago by
JourneyToAbyss
▴ 240
0
votes
0
replies
139
views
Writing genepop from genind
R
genepop
genind
graph4lg
stacks
2 days ago by
eaabbott0
• 0
3
votes
4
replies
2.0k
views
Remove all entries with duplicate names from fastq file?
fastq
illumina
duplicate
updated 3 days ago by
Charles-Alexandre Roy
▴ 50 • written 3.9 years ago by
wormball
▴ 10
1
vote
1
reply
177
views
Copy Number Variants with CNVKit
CVNs
Somatic_variant
Recommendations
CNVKit
updated 2 days ago by
GenoMax
151k • written 3 days ago by
AIMAR
• 0
0
votes
0
replies
148
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
3 days ago by
aj
• 0
0
votes
0
replies
150
views
TEtranscripts analysis
TEtranscripts
3 days ago by
frarodmar17
• 0
0
votes
0
replies
155
views
CVNkit call commande
CVNs
CNVKit
Somatic_variant
3 days ago by
AIMAR
• 0
0
votes
6
replies
347
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
4 hours ago by
n_navy
• 0
0
votes
1
reply
216
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq
DEGs
updated 2 days ago by
manaswwm
▴ 570 • written 3 days ago by
noodlejackson
▴ 40
2
votes
3
replies
478
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 3 days ago by
GenoMax
151k • written 13 days ago by
Ambuj
• 0
0
votes
0
replies
156
views
News:
Online course: Introduction to R and Bioconductor
R
Bioconductor
Genomics
3 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
155
views
IM-fusion data analysis
IM-fusion
3 days ago by
frarodmar17
• 0
0
votes
4
replies
316
views
error in reading codelink data
readcodelinkset
1 day ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
230
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 3 days ago by
Aspire
▴ 380 • written 3 days ago by
stalo.lili
• 0
7
votes
5
replies
678
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 2 days ago by
cmdcolin
★ 4.2k • written 18 days ago by
Pierre Lindenbaum
166k
8
votes
6
replies
3.3k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 3 days ago by
GenoMax
151k • written 12.1 years ago by
Mary
11k
121,184 results • Page
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Recent Votes
Answer: PRS result interpretation
Answer: PRS result interpretation
Answer: Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness
Answer: Transform a GTF file into a data frame in R
Handbooks for Bioinformatics Ninjas
Handbooks for Bioinformatics Ninjas
A: Removal of 'low' counts before DESeq2 - what threshold?
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fred.s.kremer
▴ 110
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j.k3096
• 0
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wo_li
▴ 10
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Recent Replies
Comment: PRS result interpretation
by
trkfs
▴ 10
Much thanks for your reply. If I could ask - what would be the best way or what kind of data is typically needed to obtain a PRS score that…
Answer: PRS result interpretation
by
Sam
★ 4.8k
Unfortunately, PRS is a population measurement, in that, it rarely make sense to generate an individual prediction value and compared to an…
Comment: FraserDataSet() error in FRASER
by
n_navy
• 0
It looks like that; sampleID condition batch bamFile 3618-A control batch1 RP24-190-3618-A_S639_L002_2pass_Aligne…
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
GenoMax
151k
Can you also include a link to the page/source where this spreadsheet came from? A random google docs link seems a bit dodgy to click on an…
Comment: Trimmomatic command
by
dthorbur
★ 3.0k
Please provide more information. You've shown a command to trim PE data, but haven't said what you're trying to achieve. But yes, trimming …
Answer: More rare variants than common variants
by
LChart
4.9k
> Is it normal to have more rare variants (MAF<0.01) than common variants in a large dataset like this? Yes, this is the site frequency sp…
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
Arup Ghosh
3.3k
Check this spreadsheet. https://docs.google.com/spreadsheets/d/14lrNr9B2vCGLIBXwnrgKgZGneDVSnHd1x_tlXMrmbM8/edit?gid=0#gid=0
Comment: RNA-seq analysis
by
Gordon Smyth
★ 8.0k
Yes, the code I gave you will work on any BAM file. In general, strand information is used only when assigning read alignments to genes, no…
Comment: RNA-seq analysis
by
SEJAL
• 0
Will it work on BAM files that I obtained from HISAT2 with default option of strandedness, i.e. unstranded? Or STAR aligned BAM files (whic…
Comment: CDS phase 0,1,2 in GFF format
by
wo_li
▴ 10
Hi Pierre, I'm new to the GFF format and learning from your post. I wonder if I understand correctly, that each CDS regions doesn't need t…
Answer: Question about vg giraffe, vg surject and Visualization tool for mapping result
by
Jordan M Eizenga
▴ 740
`vg surject` doesn't do a full realignment of the read against the linear reference. In general, it tries to preserve as much of the graph …
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
GenoMax
151k
Finding recent **public** human tumor sequence data (and VCF) is going to be rare because of patient privacy concerns. You could sign up an…
Comment: Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness
by
LChart
4.9k
Thanks for the historical blah! Happy to be reader #14. Hopefully the past 20 years have demonstrated that a statement like "Figure 2 show…
Comment: FraserDataSet() error in FRASER
by
marco.barr
▴ 170
Can you show the `colData` data? It’s important that `colData$sampleID` is identical to `rownames(colData)` and to the sample names in `jun…
Comment: Single cell expression and accessibility integration using cellxgene data
by
1769mkc
★ 1.3k
thank you for the resources, will try and update
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