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184 results • Page
3 of 4
Sort: Views
Rank
Views
Votes
Replies
0
votes
3
replies
217
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 days ago by
GenoMax
142k • written 5 days ago by
RNAseqer
▴ 270
2
votes
3
replies
216
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 4 days ago by
Ram
43k • written 4 days ago by
Prawesh
• 0
1
vote
2
replies
212
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 5 days ago by
colindaven
6.4k • written 6 days ago by
ramendra.sarma
• 0
1
vote
3
replies
208
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
shpak.max
▴ 50
0
votes
2
replies
208
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
0
votes
3
replies
207
views
How to access GWAVA software of data
GWAVA
updated 4 days ago by
GenoMax
142k • written 4 days ago by
nonaddldy
▴ 10
2
votes
2
replies
206
views
Genome Visualization Tools
bacterial
genome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
dlera.lozano
▴ 10
4
votes
1
reply
206
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 days ago by
J.
▴ 40
2
votes
2
replies
201
views
genome finishing
finishing
genome
updated 3 days ago by
nd48
▴ 20 • written 3 days ago by
trezini
• 0
0
votes
1
reply
197
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 5 days ago by
chrchang523
10k • written 10 days ago by
analyst
▴ 50
3
votes
2
replies
196
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 5 days ago by
ATpoint
82k • written 5 days ago by
jennyp0706
• 0
0
votes
3
replies
194
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 5 days ago by
Ram
43k • written 5 days ago by
yau
• 0
1
vote
1
reply
193
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 2 days ago by
Ram
43k • written 3 days ago by
dwpeng
▴ 10
0
votes
2
replies
192
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 days ago by
melissa.joubert
• 0
0
votes
2
replies
191
views
Trimming tool
Trimmer
tool
updated 1 day ago by
ntsopoul
▴ 60 • written 1 day ago by
GeneC
• 0
0
votes
2
replies
188
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 1 day ago by
LauferVA
4.2k • written 1 day ago by
ijarne
• 0
1
vote
1
reply
187
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
2
votes
2
replies
187
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 2 days ago by
Ram
43k • written 3 days ago by
jsmith120f
• 0
1
vote
1
reply
186
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
0
votes
2
replies
184
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
4 days ago by
IdaHao0921
• 0
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
5 days ago by
Emily
▴ 20
1
vote
2
replies
183
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
1
vote
1
reply
182
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
0
votes
1
reply
177
views
How can I calculate the OS of each patient?
overall-survival
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Pedro
• 0
1
vote
1
reply
175
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Pegasus
▴ 100
0
votes
1
reply
173
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 2 days ago by
Michael
54k • written 3 days ago by
mgranada3
▴ 30
0
votes
1
reply
172
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 2 days ago by
DGTool
▴ 20 • written 4 days ago by
iqra
• 0
0
votes
1
reply
171
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
Luqman
• 0
0
votes
1
reply
170
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Ezequiel
• 0
2
votes
1
reply
166
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 6 hours ago by
Gordon Smyth
★ 7.2k • written 1 day ago by
marineandriot
• 0
0
votes
3
replies
167
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 days ago by
Esraa
• 0
0
votes
1
reply
163
views
consensus sequence calling
consensus
updated 5 days ago by
bk11
★ 2.5k • written 5 days ago by
Ghada
• 0
0
votes
1
reply
162
views
How to process Bulk WES data?
WES
WGS
updated 5 days ago by
GenoMax
142k • written 5 days ago by
wyuan37
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
1
reply
159
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 5 days ago by
Philipp Bayer
8.5k • written 6 days ago by
samRayne
• 0
0
votes
1
reply
158
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 5 days ago by
GenoMax
142k • written 6 days ago by
octpus616
▴ 100
0
votes
1
reply
154
views
Add line under stat test
stats
R
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
Ghada
• 0
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 5 days ago by
Ram
43k • written 5 days ago by
eking28
• 0
0
votes
1
reply
151
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Lélé
▴ 10
0
votes
1
reply
151
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 5 days ago by
Ram
43k • written 12 days ago by
David
• 0
0
votes
1
reply
149
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 2 days ago by
Papyrus
★ 2.9k • written 3 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
148
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 days ago by
sansan_96
▴ 90
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
0
votes
0
replies
146
views
select set of intervals that cover a genomic region
GRanges
bed
3 days ago by
ntsopoul
▴ 60
0
votes
1
reply
146
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 4 days ago by
LauferVA
4.2k • written 4 days ago by
graeme.thorn
▴ 100
1
vote
1
reply
144
views
constructing pangenome through psvcp
psvcp
pangenome
13 hours ago by
analyst
▴ 50
0
votes
1
reply
144
views
Splitting Seurat object by sample layers
seurat
updated 5 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
2
votes
0
replies
143
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
5 days ago by
Biostar
2.8k
0
votes
1
reply
141
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 1 day ago by
dthorbur
★ 2.0k • written 1 day ago by
Umer
▴ 50
184 results • Page
3 of 4
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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