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120,119 results • Page
1 of 2403
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
36
views
Nothing happens when running GATK VCF Validate Variants. Output warning: processed 0 (zero) total variants
GATK
VCF
snp
ValidateVariants
1 hour ago by
maikejet
• 0
0
votes
1
reply
104
views
Annotate GWAS result gene function from GFF file
gwas
gff
gff3
annotation
updated 7 hours ago by
lieven.sterck
15k • written 21 hours ago by
alnus
• 0
0
votes
0
replies
55
views
WGCNA sample-data preprocessing order
gene-expression
wcgna
microarray
network
data-preprocessing
12 hours ago by
Reuben
• 0
8
votes
5
replies
248
views
6 follow
STAR aligner - Is this still maintained?
STAR
aligner
rnaseq
updated 5 hours ago by
ATpoint
86k • written 1 day ago by
Joshi
• 0
825
votes
169
replies
164k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.3k • written 8.1 years ago by
Istvan Albert
102k
6
votes
3
replies
1.2k
views
drug sensitivity prediction
deseq2
oncopredict
R
drug
updated 1 day ago by
Luka
• 0 • written 2.2 years ago by
luffy
▴ 130
0
votes
0
replies
76
views
VCFfiltering
VCF
BCFtools
FreeBayes
updated 10 hours ago by
GenoMax
148k • written 1 day ago by
Peter
• 0
0
votes
0
replies
93
views
Clumping- cannot mtfrm
clumping
MR
updated 1 day ago by
GenoMax
148k • written 1 day ago by
sp
• 0
0
votes
0
replies
118
views
Analysis and Verification of Mathematical Equations in the Theory of Consciousness
Consciousness
brian
Neuron
neurobiology
updated 1 day ago by
GenoMax
148k • written 1 day ago by
steklolampa
• 0
0
votes
0
replies
123
views
Genetic Trio Phasing with EAGLE2 using hg38
trios
haplotype
phasing
genetics
2 days ago by
heskett
▴ 110
5
votes
3
replies
257
views
b37 liftover
b37
liftover
1 day ago by
spesks
• 0
0
votes
0
replies
117
views
Plugging output files from phyluce phasing workflow into Structure
phyluce
uce
bam
phasing
structure
2 days ago by
gabe.somarriba
• 0
0
votes
0
replies
118
views
gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
header
pacbio
bam
basecaller
gcpp
2 days ago by
therosng
• 0
0
votes
1
reply
159
views
circos ignoring the ticks and plots
diagram
circos
updated 2 days ago by
GenoMax
148k • written 2 days ago by
baibhu1234
• 0
3
votes
4
replies
310
views
Strange offsetting in deeptools?
deeptools
1 day ago by
Elijah
▴ 10
0
votes
3
replies
212
views
Merging gvcf files between Dragen and other calling tools
gvcf
merge
bcftools
updated 2 days ago by
Pierre Lindenbaum
165k • written 2 days ago by
tacrolimus
▴ 140
7
votes
6
replies
364
views
Download SRA raw data using efetch
sra-toolkit
efetch
biopython
2 days ago by
biofysikos
• 0
0
votes
7
replies
295
views
Issue with CIBERSORTx Error 139
CIBERSORTX
docker
error193
updated 2 days ago by
jared.andrews07
★ 18k • written 2 days ago by
Hamdache
• 0
0
votes
0
replies
126
views
Repeat Modeler Database Generation
masker
modeler
genome
fungus
repeat
2 days ago by
SomeOne
▴ 160
0
votes
0
replies
117
views
How to scale data matrix in Seurat
Scale
2 days ago by
frarodmar17
• 0
0
votes
1
reply
167
views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly
genoem
fungus
HiC
sequencing
updated 2 days ago by
GenoMax
148k • written 2 days ago by
SomeOne
▴ 160
0
votes
1
reply
150
views
Box plot of gene expression data
boxplot
updated 2 days ago by
ATpoint
86k • written 2 days ago by
a.stef.44
▴ 10
1
vote
2
replies
311
views
Questions regarding GSEA - clusterProfiler
RNA-seq
GSEA
2 days ago by
CaroH
▴ 10
0
votes
0
replies
153
views
Account for Clinical Variables in RNA-Seq Analysis
edgeR
Batch
effect
2 days ago by
fabian
▴ 10
0
votes
2
replies
225
views
bioinformatics tutorial on Oxford
oxford
nanopore
updated 2 days ago by
GenoMax
148k • written 2 days ago by
Bogdan
★ 1.4k
3
votes
0
replies
167
views
Tutorial:
Step by step tutorial to replicate a genomics figure
R
Unix
ChIP-seq
bioconductor
2 days ago by
Ming Tommy Tang
★ 4.5k
0
votes
0
replies
141
views
How to determine which pangenome nodes correspond to hg38 coordinates?
pangenome
reference-genome
hg38
genomics
3 days ago by
a5864557
• 0
0
votes
0
replies
141
views
LDhat analysis pipeline
recombination
LDhat
3 days ago by
chaudharyc61
▴ 100
2
votes
7
replies
608
views
6 follow
Parsing error in sam file when converting to bam
samtools
bwa
fastq
bam
sam
updated 3 days ago by
GenoMax
148k • written 10 days ago by
emily.coger
• 0
4
votes
1
reply
768
views
GATK site filtering: when should I use VQSR or hard filtering?
VQSR
GATK
updated 3 days ago by
alba
• 0 • written 3.2 years ago by
samuelandjw
▴ 270
0
votes
1
reply
179
views
Missing `pro_ref` Folder in PICRUSt2 Default Files
github
PICRUSt2
updated 3 days ago by
Ram
44k • written 3 days ago by
ameeraelshinawy
• 0
2
votes
1
reply
200
views
How to Display Metadata on IGV Visualizations
Integrative-Genomics-Viewer
IGV
updated 3 days ago by
Ram
44k • written 3 days ago by
luminea
▴ 10
0
votes
3
replies
263
views
Understanding how to deal with Brain snRNA-seq data
scanpy
python
single-cell
anndata
RNA
updated 2 days ago by
Ming Tommy Tang
★ 4.5k • written 3 days ago by
JACKY
▴ 170
2
votes
2
replies
276
views
RNA-seq combined treatment interaction experiment design
RNA-seq
DESeq2
updated 3 days ago by
Ram
44k • written 4 days ago by
Manko47
▴ 10
0
votes
0
replies
169
views
Forum:
Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping
variants
updated 3 days ago by
GenoMax
148k • written 3 days ago by
Ian
6.1k
23
votes
11
replies
16k
views
6 follow
CIBERSORT deconvolution advice
CIBERSORT
CIBERSORTx
deconvolution
updated 3 days ago by
Nguyen
• 0 • written 4.8 years ago by
joker33
▴ 150
0
votes
1
reply
334
views
News:
In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
Transcriptomics
Workshop
RNA-Seq
3 days ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
163
views
Sesame Data ExperimentHub and related issues
caching
sesame
methylation
updated 3 days ago by
GenoMax
148k • written 3 days ago by
jain72744
▴ 10
0
votes
0
replies
163
views
Unable to link peaks to genes for multiomics data
multiome
multiomics
linkPeaks
Signac
10X
3 days ago by
sribas.chowdhury888
• 0
0
votes
0
replies
172
views
GWAS for Klebsiella isolates
technical
help
GWAS
3 days ago by
Bahnie
• 0
0
votes
0
replies
164
views
CoCoRV - Which file from gnomAD as control
Variants
Rare
WES
4 days ago by
andrebolerbarros
• 0
2
votes
1
reply
229
views
SNP/kb in chromosome wise
Variant
SNP
Calling
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
adarsh_munna
▴ 50
0
votes
0
replies
171
views
time to event GWAS
signals
independent
updated 4 days ago by
GenoMax
148k • written 4 days ago by
JJ
• 0
3
votes
9
replies
493
views
single-cell zeros handling, inputation and filtration
zeros
single-cell
updated 3 days ago by
jared.andrews07
★ 18k • written 4 days ago by
frarodmar17
• 0
0
votes
3
replies
261
views
submitting to SRA database
files
pod5
SRA
updated 4 days ago by
ATpoint
86k • written 4 days ago by
baibhu1234
• 0
4
votes
3
replies
349
views
Flattened TSS enrichment x unique fragments from scATAC experiment
ATAC
updated 4 days ago by
jared.andrews07
★ 18k • written 5 days ago by
forestyang
• 0
1
vote
1
reply
227
views
biopython UI?
biopython
updated 4 days ago by
Joe
22k • written 4 days ago by
tada
• 0
2
votes
6
replies
388
views
determine softmask regions from FASTA
BED
FASTA
softmask
updated 3 days ago by
lieven.sterck
15k • written 4 days ago by
Matteo Ungaro
▴ 110
0
votes
4
replies
343
views
Number of reads supporting a structural variant value in Dragen structural variant calling output
Structural
VCF
variants
Manta
updated 3 days ago by
benformatics
4.1k • written 4 days ago by
ieie
▴ 10
3
votes
2
replies
484
views
Strategy for mapping rat and human gene symbols from scRNA-seq data - dealing with inconsistent nomenclature
Orthologs
scRNAseq
updated 4 days ago by
ATpoint
86k • written 6 days ago by
dxj294
• 0
120,119 results • Page
1 of 2403
Recent Votes
Comment: STAR aligner - Is this still maintained?
Answer: drug sensitivity prediction
A: How Do I Convert Fbgn (Flybase Ids) To Gene Symbols In R/Bioconductor?
How Do I Convert Fbgn (Flybase Ids) To Gene Symbols In R/Bioconductor?
Answer: STAR aligner - Is this still maintained?
Answer: STAR aligner - Is this still maintained?
Answer: STAR aligner - Is this still maintained?
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Recent Replies
Comment: STAR aligner - Is this still maintained?
by
ATpoint
86k
Definitely not worth the effort unless there is a critical bug that concerns your specific analysis AND Alex Dobin by personal email will n…
Comment: STAR aligner - Is this still maintained?
by
lieven.sterck
15k
I'm with Rob on that option 4 :) Moreover I would , to some extend, also vote against option 1, mainly given your lack in C/C++ and conse…
Answer: Annotate GWAS result gene function from GFF file
by
lieven.sterck
15k
If the info you need is available in the GFF file then yes it is possible, however according to GFF specs it is not a necessity to put this…
Comment: STAR aligner - Is this still maintained?
by
dsull
★ 7.2k
The spam only started about 2-3 weeks ago (during the holidays) by automated spam bots. I think STAR will be ok haha and, yeah, I don't thi…
Comment: drug sensitivity prediction
by
DareDevil
★ 4.3k
Inputs can be data converted in log2 scale or vst.
Comment: STAR aligner - Is this still maintained?
by
GenoMax
148k
Every software package reaches a state where it does what most (dare I say 90+%) people want it to do in a stable fashion. So not seeing ne…
Answer: STAR aligner - Is this still maintained?
by
Rob
7.0k
I think the maintenance frequency has decreased as Alex has moved on to a new job. However, I an my team are working to make several contr…
Comment: drug sensitivity prediction
by
Luka
• 0
Hi, im working with OncoPredict. Can you tell me if you have any info on the input of counts in to the algorithm. Do I need to log transfor…
Comment: b37 liftover
by
spesks
• 0
Thank you! renaming chrs according to hg19 and using hg19 chain files helped.
Comment: Strange offsetting in deeptools?
by
Elijah
▴ 10
Oh I see! Yes, this is very clear, thank you so much for the in-depth answer :) I think what I was missing was exactly what you said - tha…
Comment: Strange offsetting in deeptools?
by
rfran010
★ 1.3k
Yes, the mix up is maybe that your RNA can come from plus or minus strand. Depending on which strand the RNA originated from, Read1 will c…
Comment: Strange offsetting in deeptools?
by
Elijah
▴ 10
Thank you for your reply! Does filterRNAstrand not remove read 2? From the documentation for filterRNAstrand: "Selects RNA-seq reads (sin…
Comment: Issue with CIBERSORTx Error 139
by
jared.andrews07
★ 18k
I believe the site was down earlier today for a bit as well, so it may have been on their end. They have a banner saying user login is now …
Answer: b37 liftover
by
Giulio Genovese
▴ 600
Using [BCFtools/liftover](https://doi.org/10.1093/bioinformatics/btae038) will automatically take care of: - flexible contig names (e.g. …
Comment: circos ignoring the ticks and plots
by
GenoMax
148k
Please copy and paste the actual code instead of posting screenshots. You can format the text as `code` by using `101010` button in edit wi…
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