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117,055 results • Page
3 of 2342
Sort: Rank
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Views
Votes
Replies
0
votes
4
replies
341
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 4 days ago by
Tony
• 0 • written 5 days ago by
vk
▴ 10
1
vote
5
replies
335
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 4 days ago by
Ram
44k • written 5 days ago by
manuelmourato25
• 0
3
votes
4
replies
427
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
758
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 days ago by
egascon
• 0
1
vote
1
reply
206
views
API kegg - IndexError: list index out of range
kegg
API
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
150
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
5 days ago by
Novogene
▴ 420
0
votes
0
replies
146
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
5 days ago by
ebertomeup
• 0
0
votes
3
replies
289
views
Sam file Header problem
Sam
Header
problem
file
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
saifulislam99121
• 0
1
vote
3
replies
296
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 4 days ago by
Ram
44k • written 6 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
596
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 5 days ago by
valdirbarth
▴ 20 • written 13 months ago by
Salomé
• 0
0
votes
0
replies
150
views
select set of intervals that cover a genomic region
GRanges
bed
5 days ago by
ntsopoul
▴ 60
1
vote
1
reply
203
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 4 days ago by
Ram
44k • written 5 days ago by
dwpeng
▴ 10
0
votes
2
replies
219
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
1 day ago by
Luqman
• 0
2
votes
3
replies
263
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 4 days ago by
Ram
44k • written 5 days ago by
sooni
▴ 20
0
votes
5
replies
345
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
20 hours ago by
mavy
▴ 10
1
vote
1
reply
254
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
5 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 5 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
182
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 5 days ago by
Michael
54k • written 5 days ago by
mgranada3
▴ 30
0
votes
1
reply
162
views
Add line under stat test
stats
R
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
Ghada
• 0
1
vote
5
replies
814
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
115
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 5 days ago by
GenoMax
142k • written 6 days ago by
Rodolfo Adrián
• 0
1
vote
3
replies
213
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
shpak.max
▴ 50
2
votes
4
replies
287
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 6 days ago by
yura.grabovska
▴ 90 • written 6 days ago by
ev97
▴ 20
1
vote
16
replies
776
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 3 days ago by
GenoMax
142k • written 6 days ago by
hophuquy0944
• 0
0
votes
4
replies
254
views
Sequencing Depth (Read Depth) Calculations
depth
5 days ago by
LucisTheFather
• 0
0
votes
1
reply
144
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
6 days ago by
asalimih
▴ 60
0
votes
0
replies
115
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
6 days ago by
jway
• 0
2
votes
2
replies
195
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 5 days ago by
Ram
44k • written 6 days ago by
jsmith120f
• 0
2
votes
2
replies
211
views
genome finishing
finishing
genome
updated 6 days ago by
nd48
▴ 30 • written 6 days ago by
trezini
• 0
1
vote
5
replies
239
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
biology_inform
▴ 50
1
vote
4
replies
308
views
Add stats to boxplot in R
stats
R
5 days ago by
Ghada
• 0
0
votes
1
reply
164
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 days ago by
Papyrus
★ 2.9k • written 6 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
160
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 5 days ago by
GenoMax
142k • written 6 days ago by
Lélé
▴ 10
0
votes
5
replies
318
views
calculating genomic coverage/ base overlap in R
genomics
updated 3 days ago by
1769mkc
★ 1.2k • written 6 days ago by
Xbox_27
• 0
1
vote
5
replies
281
views
Annotating file using bcftools
annotation
plink
bcftools
5 days ago by
kl
▴ 10
0
votes
9
replies
385
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
5 days ago by
njornet
▴ 20
0
votes
3
replies
182
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
6 days ago by
Esraa
• 0
3
votes
3
replies
245
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Alexandra
• 0
3
votes
1
reply
335
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 6 days ago by
dariober
14k • written 7 days ago by
Holly
▴ 30
1
vote
4
replies
301
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
5 days ago by
Arton
▴ 10
0
votes
0
replies
100
views
ReactomeGSA
ReactomeGSA
6 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
89
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
6 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
299
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 5 days ago by
GenoMax
142k • written 6 days ago by
chrisk
• 0
0
votes
1
reply
182
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 5 days ago by
DGTool
▴ 20 • written 6 days ago by
iqra
• 0
0
votes
0
replies
105
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Dude
• 0
0
votes
0
replies
100
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
6 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
220
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 6 days ago by
colindaven
6.4k • written 6 days ago by
mbrav005
• 0
0
votes
1
reply
153
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
6 days ago by
sansan_96
▴ 90
1
vote
2
replies
243
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
5 days ago by
MarcosCosta
• 0
2
votes
2
replies
212
views
Genome Visualization Tools
bacterial
genome
updated 6 days ago by
GenoMax
142k • written 6 days ago by
dlera.lozano
▴ 10
117,055 results • Page
3 of 2342
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Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
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Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
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Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
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★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
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I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
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Bjorn
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