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694 results • Page
3 of 14
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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
43k • 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
813
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 5 days ago by
Rodolfo Adrián
• 0
1
vote
3
replies
212
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
shpak.max
▴ 50
2
votes
4
replies
282
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 5 days ago by
yura.grabovska
▴ 90 • written 5 days ago by
ev97
▴ 20
1
vote
16
replies
767
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 2 days ago by
GenoMax
142k • written 5 days ago by
hophuquy0944
• 0
0
votes
4
replies
252
views
Sequencing Depth (Read Depth) Calculations
depth
5 days ago by
LucisTheFather
• 0
0
votes
1
reply
143
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
5 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
5 days ago by
jway
• 0
2
votes
2
replies
194
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 4 days ago by
Ram
43k • written 5 days ago by
jsmith120f
• 0
2
votes
2
replies
209
views
genome finishing
finishing
genome
updated 5 days ago by
nd48
▴ 30 • written 6 days ago by
trezini
• 0
1
vote
5
replies
233
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
biology_inform
▴ 50
1
vote
4
replies
303
views
Add stats to boxplot in R
stats
R
5 days ago by
Ghada
• 0
0
votes
1
reply
159
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 days ago by
Papyrus
★ 2.9k • written 5 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
158
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 4 days ago by
GenoMax
142k • written 5 days ago by
Lélé
▴ 10
0
votes
5
replies
315
views
calculating genomic coverage/ base overlap in R
genomics
updated 2 days ago by
1769mkc
★ 1.2k • written 5 days ago by
Xbox_27
• 0
1
vote
5
replies
277
views
Annotating file using bcftools
annotation
plink
bcftools
4 days ago by
kl
▴ 10
0
votes
9
replies
380
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
5 days ago by
njornet
▴ 20
0
votes
3
replies
180
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
242
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
332
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
298
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
181
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
104
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
99
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
6 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
218
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
240
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
2
votes
3
replies
226
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 6 days ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
302
views
Using ggplotly in R
ggplot
ggplotly
updated 5 days ago by
jared.andrews07
★ 17k • written 6 days ago by
jen
▴ 10
1
vote
2
replies
241
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
4 days ago by
bioinfo
▴ 150
0
votes
3
replies
278
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 6 days ago by
noodle
▴ 580 • written 6 days ago by
doramora
▴ 10
0
votes
1
reply
151
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 6 days ago by
LauferVA
4.2k • written 6 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
209
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 days ago by
melissa.joubert
• 0
4
votes
1
reply
217
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
6 days ago by
J.
▴ 40
0
votes
0
replies
116
views
Is there a real ground truth for CNV data?
CNV
6 days ago by
jennyp0706
• 0
0
votes
3
replies
226
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 days ago by
GenoMax
142k • written 7 days ago by
RNAseqer
▴ 270
1
vote
1
reply
152
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 7 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
8
replies
482
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 3 days ago by
Alex Reynolds
35k • written 7 days ago by
ntsopoul
▴ 60
0
votes
3
replies
217
views
How to access GWAVA software of data
GWAVA
updated 6 days ago by
GenoMax
142k • written 7 days ago by
nonaddldy
▴ 10
0
votes
2
replies
234
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
5 days ago by
Chen
• 0
1
vote
1
reply
182
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 7 days ago by
ATpoint
82k • written 7 days ago by
Pegasus
▴ 100
0
votes
1
reply
137
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 6 days ago by
Ram
43k • written 7 days ago by
Emily
▴ 20
694 results • Page
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Recent Votes
Comment: What marks a De-Novo Genome assembly as FAILED?
A: How to extract specific chromosome from vcf file
A: How To Filter Mapped Reads With Samtools
C: Filtering A Sam File For Quality Scores
A: Filtering A Sam File For Quality Scores
Comment: Super ehancers
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
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by
Klaus S
▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
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by
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Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
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marco.barr
▴ 130
what a pity...
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▴ 20
Yes, I can. But there are only two factors that affect my data PCA distribution: groups and donor. And the rest is regarded as residual. …
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by
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6.4k
Please delete this as it has nothing to do with the topic of this forum, bioinformatics. Thanks
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if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
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you should ask : https://github.com/nf-core/sarek/issues/
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https://github.com/gatk-workflows ?
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Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files
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Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
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Thank you so much Dave.
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