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85 results • Page
1 of 2
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Views
Votes
Replies
5
votes
7
replies
502
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 20
3
votes
3
replies
293
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
3
votes
2
replies
199
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 6 days ago by
ATpoint
82k • written 6 days ago by
jennyp0706
• 0
2
votes
2
replies
252
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
txema.heredia
▴ 130
2
votes
9
replies
1.0k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
1 hour ago by
LauferVA
4.2k
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
1
vote
1
reply
164
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
1
vote
4
replies
352
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 6 days ago by
Vijith
▴ 30
1
vote
1
reply
278
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 17 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
1
reply
192
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 13 days ago by
sarumonsus
▴ 10
1
vote
5
replies
335
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
1
vote
0
replies
99
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
6 days ago by
tomas4482
▴ 400
1
vote
1
reply
196
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
mirwa.zidi93
• 0
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
1
vote
1
reply
148
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
1
vote
4
replies
320
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 10 days ago by
cput
• 0
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
355
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
95
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
5 days ago by
Spring
• 0
0
votes
2
replies
187
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
0
votes
4
replies
263
views
Galaxy StringTie error
stringtie
galaxy
5 days ago by
trkfs
• 0
0
votes
3
replies
209
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
0
votes
0
replies
113
views
Is there a real ground truth for CNV data?
CNV
5 days ago by
jennyp0706
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
4 days ago by
brunofelicianodeomena
• 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
1
reply
149
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 days ago by
sansan_96
▴ 90
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
0
votes
0
replies
98
views
ReactomeGSA
ReactomeGSA
4 days ago by
Shaimaa Gamal
▴ 10
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
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
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
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
0
votes
9
replies
606
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
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
0
replies
147
views
select set of intervals that cover a genomic region
GRanges
bed
3 days ago by
ntsopoul
▴ 60
0
votes
0
replies
140
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 days ago by
ebertomeup
• 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
173
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
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
0
replies
139
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
0
votes
1
reply
193
views
How can I calculate the OS of each patient?
overall-survival
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pedro
• 0
0
votes
0
replies
140
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
3 days ago by
Jsarria.EEAD
• 0
0
votes
0
replies
138
views
Use of ichor CNA
Dog
CNA
genome
2 days ago by
sainavyav22
• 0
0
votes
0
replies
130
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
2 days ago by
O.rka
▴ 720
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
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
0
replies
111
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
2 days ago by
Varsha
• 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
0
votes
2
replies
222
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
85 results • Page
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Recent Votes
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)
Answer: RNAseq coverage vs depth for transcript isoform expression?
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?
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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
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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
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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
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★ 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
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82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
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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
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★ 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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