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320 results • Page
1 of 7
Sort: Votes
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Views
Votes
Replies
5
votes
5
replies
323
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by
Chris
▴ 280
5
votes
7
replies
500
views
RNA seq analysis
DESeq
RNA-seq
3 days ago by
Jacek
▴ 20
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
19 days ago by
anna
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 12 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
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
7
replies
421
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
19 days ago by
salias
• 0
3
votes
3
replies
554
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 28 days ago by
swbarnes2
14k • written 29 days ago by
noodle
▴ 580
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
3
votes
5
replies
346
views
Generating mpileup file using samtools
mpileup
samtools
updated 15 days ago by
Joe
21k • written 15 days ago by
Ruqaiya
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 10 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
4
replies
325
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
3
votes
1
reply
207
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 8 days ago by
dthorbur
★ 2.0k • written 9 days ago by
Eren
• 0
3
votes
8
replies
616
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 days ago by
Qroid
▴ 40
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 14 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
2
votes
5
replies
790
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 28 days ago by
Jesse
▴ 770 • written 29 days ago by
Ann
★ 2.4k
2
votes
3
replies
331
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 15 days ago by
dthorbur
★ 2.0k • written 15 days ago by
Vijith
▴ 30
2
votes
2
replies
337
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 24 days ago by
Ram
43k • written 25 days ago by
v.berriosfarias
▴ 140
2
votes
2
replies
232
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
944
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 25 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
2
votes
4
replies
384
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
24 days ago by
samuelkalandarov2002
▴ 10
2
votes
5
replies
543
views
Marking duplicates using UMIs
Deduplication
UMI
updated 26 days ago by
i.sudbery
19k • written 28 days ago by
Lipika
• 0
2
votes
2
replies
246
views
PDB related issue
rcsb
pdb
updated 20 days ago by
noodle
▴ 580 • written 20 days ago by
Nafi
• 0
2
votes
2
replies
251
views
Raw counts using stringtie
stringtie
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ahmad.sajad4541
• 0
2
votes
3
replies
342
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 13 days ago by
Yoosef
▴ 60
2
votes
5
replies
957
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 19 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 15 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
1
vote
1
reply
529
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
29 days ago by
renan.igor
• 0
1
vote
1
reply
162
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 9 days ago by
andres.firrincieli
3.6k • written 9 days ago by
kacollier
▴ 30
1
vote
0
replies
175
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
22 days ago by
KABILAN
▴ 70
1
vote
1
reply
224
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
2
replies
229
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
1
reply
458
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 27 days ago by
Gordon Smyth
★ 7.2k • written 4 weeks ago by
Chris
▴ 280
1
vote
0
replies
143
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
9 days ago by
Shae
▴ 10
1
vote
0
replies
195
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
23 days ago by
rohitsatyam102
▴ 860
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
23 days ago by
ahmad.sajad4541
• 0
1
vote
3
replies
451
views
PCA plot
DESeq2
PCAplot
updated 20 days ago by
LauferVA
4.2k • written 23 days ago by
Aaliya
▴ 10
1
vote
4
replies
307
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 13 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
1
vote
2
replies
194
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
11 days ago by
robert.flynn.21
• 0
1
vote
3
replies
264
views
STAR aligner error
RNA-seq
STAR
slurm
updated 10 days ago by
Ram
43k • written 11 days ago by
M.
▴ 30
1
vote
3
replies
330
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 18 days ago by
GenoMax
142k • written 18 days ago by
jeffrey.maurer.informatics
• 0
1
vote
8
replies
557
views
Downsampling fastq file
downsample
fastq
18 days ago by
marco.barr
▴ 130
1
vote
6
replies
412
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 15 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
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
0
replies
98
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
5 days ago by
tomas4482
▴ 400
1
vote
0
replies
178
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
9 days ago by
eebloom
▴ 80
1
vote
1
reply
176
views
student
epitranscriptomics
updated 11 days ago by
ATpoint
82k • written 11 days ago by
useriwa
• 0
1
vote
2
replies
257
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 18 days ago by
Ram
43k • written 18 days ago by
Ravita
• 0
1
vote
1
reply
176
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
16
replies
719
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 10 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
320 results • Page
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Recent Votes
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?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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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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