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674 results • Page
2 of 14
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
140
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 days ago by
ebertomeup
• 0
0
votes
3
replies
279
views
Sam file Header problem
Sam
Header
problem
file
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
saifulislam99121
• 0
1
vote
3
replies
279
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 2 days ago by
Ram
43k • written 4 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
594
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 3 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
147
views
select set of intervals that cover a genomic region
GRanges
bed
3 days ago by
ntsopoul
▴ 60
1
vote
1
reply
195
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
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
2
votes
3
replies
253
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 2 days ago by
Ram
43k • written 3 days ago by
sooni
▴ 20
0
votes
4
replies
282
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
3 days ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 3 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
174
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 3 days ago by
Michael
54k • written 3 days ago by
mgranada3
▴ 30
0
votes
1
reply
157
views
Add line under stat test
stats
R
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
Ghada
• 0
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
114
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Rodolfo Adrián
• 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
2
votes
4
replies
273
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 3 days ago by
yura.grabovska
▴ 90 • written 3 days ago by
ev97
▴ 20
1
vote
16
replies
738
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
0
votes
4
replies
244
views
Sequencing Depth (Read Depth) Calculations
depth
3 days ago by
LucisTheFather
• 0
0
votes
1
reply
140
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
3 days ago by
asalimih
▴ 60
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
4 days ago by
jway
• 0
2
votes
2
replies
189
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
2
votes
2
replies
202
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 4 days ago by
trezini
• 0
1
vote
5
replies
223
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
biology_inform
▴ 50
1
vote
4
replies
293
views
Add stats to boxplot in R
stats
R
3 days ago by
Ghada
• 0
0
votes
1
reply
152
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 3 days ago by
Papyrus
★ 2.9k • written 4 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
152
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Lélé
▴ 10
0
votes
5
replies
302
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
1769mkc
★ 1.2k • written 4 days ago by
Xbox_27
• 0
1
vote
5
replies
269
views
Annotating file using bcftools
annotation
plink
bcftools
3 days ago by
kl
▴ 10
0
votes
9
replies
362
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
3 days ago by
njornet
▴ 20
0
votes
3
replies
170
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
3
votes
3
replies
232
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Alexandra
• 0
3
votes
1
reply
325
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 4 days ago by
dariober
14k • written 5 days ago by
Holly
▴ 30
1
vote
4
replies
296
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
3 days ago by
Arton
▴ 10
0
votes
0
replies
98
views
ReactomeGSA
ReactomeGSA
4 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
87
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
4 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
288
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 3 days ago by
GenoMax
142k • written 4 days ago by
chrisk
• 0
0
votes
1
reply
172
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 3 days ago by
DGTool
▴ 20 • written 4 days ago by
iqra
• 0
0
votes
0
replies
100
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Dude
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
4 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
212
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
0
votes
1
reply
149
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 days ago by
sansan_96
▴ 90
1
vote
2
replies
234
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
3 days ago by
MarcosCosta
• 0
2
votes
2
replies
208
views
Genome Visualization Tools
bacterial
genome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
dlera.lozano
▴ 10
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
3
replies
291
views
Using ggplotly in R
ggplot
ggplotly
updated 4 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jen
▴ 10
1
vote
2
replies
231
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
0
votes
3
replies
268
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 4 days ago by
noodle
▴ 580 • written 5 days ago by
doramora
▴ 10
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
0
votes
2
replies
193
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
4 days ago by
melissa.joubert
• 0
674 results • Page
2 of 14
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plotting trees in R: node labels from nexus tree files
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A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
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constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
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
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82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
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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.…
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