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116,992 results • Page
2 of 2340
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
107
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 day ago by
jway
• 0
2
votes
2
replies
180
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 20 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
2
votes
2
replies
193
views
genome finishing
finishing
genome
updated 1 day ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 0
1
vote
5
replies
215
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
biology_inform
▴ 50
1
vote
4
replies
283
views
Add stats to boxplot in R
stats
R
1 day ago by
Ghada
• 0
0
votes
1
reply
144
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 23 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
146
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 20 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
4
replies
243
views
calculating genomic coverage/ base overlap in R
genomics
updated 20 hours ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
1
vote
5
replies
256
views
Annotating file using bcftools
annotation
plink
bcftools
20 hours ago by
kl
▴ 10
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
3
votes
3
replies
222
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Alexandra
• 0
1
vote
1
reply
219
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 2 days ago by
dariober
14k • written 3 days ago by
Holly
▴ 10
1
vote
4
replies
278
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
1 day ago by
Arton
▴ 10
0
votes
0
replies
92
views
ReactomeGSA
ReactomeGSA
2 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
85
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
2 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
278
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
2
replies
163
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 23 hours ago by
DGTool
▴ 20 • written 2 days ago by
iqra
• 0
0
votes
0
replies
98
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dude
• 0
0
votes
0
replies
95
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
198
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 days ago by
colindaven
6.4k • written 2 days ago by
mbrav005
• 0
0
votes
1
reply
143
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
1
vote
2
replies
209
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
1 day ago by
MarcosCosta
• 0
2
votes
2
replies
197
views
Genome Visualization Tools
bacterial
genome
updated 2 days ago by
GenoMax
142k • written 2 days ago by
dlera.lozano
▴ 10
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Prawesh
• 0
1
vote
3
replies
274
views
Using ggplotly in R
ggplot
ggplotly
updated 1 day ago by
jared.andrews07
★ 16k • written 2 days ago by
jen
▴ 10
1
vote
2
replies
222
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
18 hours ago by
bioinfo
▴ 150
0
votes
3
replies
255
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
doramora
▴ 10
0
votes
1
reply
143
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
186
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
4
votes
1
reply
200
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by
J.
▴ 40
0
votes
0
replies
109
views
Is there a real ground truth for CNV data?
CNV
2 days ago by
jennyp0706
• 0
0
votes
3
replies
210
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
1
vote
1
reply
145
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
kilcdincer
▴ 10
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
380
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
0
votes
3
replies
200
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
2
replies
220
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
1 day ago by
Chen
• 0
1
vote
1
reply
172
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pegasus
▴ 100
0
votes
1
reply
131
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 2 days ago by
Ram
43k • written 3 days ago by
Emily
▴ 20
1
vote
3
replies
267
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 16 hours ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
0
votes
0
replies
93
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
175
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
268
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by
Philipp Bayer
8.5k • written 3 days ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
218
views
Help with IGV abbreviation
igv
updated 2 days ago by
Ram
43k • written 3 days ago by
GeneC
• 0
0
votes
1
reply
160
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
1
reply
160
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
2
replies
424
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
116,992 results • Page
2 of 2340
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
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