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80 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
5
votes
7
replies
500
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
3
votes
3
replies
274
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
3
votes
2
replies
195
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 5 days ago by
ATpoint
82k • written 5 days ago by
jennyp0706
• 0
2
votes
2
replies
231
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
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 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
1
vote
4
replies
307
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 12 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
1
vote
2
replies
228
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
1
vote
4
replies
348
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 3 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
1
vote
16
replies
717
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 9 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
1
vote
1
reply
132
views
constructing pangenome through psvcp
psvcp
pangenome
8 hours ago by
analyst
▴ 50
1
vote
1
reply
185
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
1
vote
1
reply
215
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 hour ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
5
replies
311
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
1
reply
175
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
1
vote
0
replies
98
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
5 days ago by
tomas4482
▴ 400
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
4 days ago by
Emily
▴ 20
0
votes
3
replies
349
views
Snakemake wrapper issue
fastqc
snakemake
updated 4 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
94
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
4 days ago by
Spring
• 0
0
votes
2
replies
183
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
4 days ago by
IdaHao0921
• 0
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie
galaxy
4 days ago by
trkfs
• 0
0
votes
3
replies
205
views
How to access GWAVA software of data
GWAVA
updated 4 days ago by
GenoMax
142k • written 4 days ago by
nonaddldy
▴ 10
0
votes
0
replies
110
views
Is there a real ground truth for CNV data?
CNV
4 days ago by
jennyp0706
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
3 days ago by
brunofelicianodeomena
• 0
0
votes
0
replies
99
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Dude
• 0
0
votes
1
reply
147
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
3 days ago by
sansan_96
▴ 90
0
votes
2
replies
189
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 days ago by
melissa.joubert
• 0
0
votes
0
replies
95
views
ReactomeGSA
ReactomeGSA
3 days ago by
Shaimaa Gamal
▴ 10
0
votes
3
replies
166
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 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
3 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
113
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
603
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
287
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
0
votes
0
replies
139
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
0
votes
0
replies
125
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
1
reply
173
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 2 days ago by
Michael
54k • written 3 days ago by
mgranada3
▴ 30
0
votes
1
reply
171
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 2 days ago by
DGTool
▴ 20 • written 3 days ago by
iqra
• 0
0
votes
1
reply
149
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 2 days ago by
Papyrus
★ 2.9k • written 3 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
151
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Lélé
▴ 10
0
votes
0
replies
119
views
cat-bgen fail
bgenix
updated 2 days ago by
Ram
43k • written 2 days ago by
lambard
• 0
0
votes
1
reply
170
views
How can I calculate the OS of each patient?
overall-survival
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Pedro
• 0
0
votes
0
replies
119
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
2 days ago by
Jsarria.EEAD
• 0
0
votes
0
replies
114
views
Use of ichor CNA
Dog
CNA
genome
2 days ago by
sainavyav22
• 0
0
votes
0
replies
109
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
154
views
Add line under stat test
stats
R
updated 1 day ago by
Nyksubuz
▴ 20 • written 3 days ago by
Ghada
• 0
0
votes
1
reply
166
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Luqman
• 0
0
votes
0
replies
90
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
1 day ago by
Varsha
• 0
0
votes
3
replies
263
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
0
votes
2
replies
201
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
80 results • Page
1 of 2
Recent Votes
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?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
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Recent Replies
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
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
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.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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