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311 results • Page
1 of 7
Sort: Votes
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Votes
Replies
5
votes
5
replies
345
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
11 days ago by
Chris
▴ 280
5
votes
7
replies
504
views
RNA seq analysis
DESeq
RNA-seq
4 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
20 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 13 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
3
votes
3
replies
558
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 29 days ago by
swbarnes2
14k • written 4 weeks ago by
noodle
▴ 580
3
votes
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 9 days ago by
Eren
• 0
3
votes
8
replies
636
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
13 days ago by
Qroid
▴ 40
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 17 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
5
replies
352
views
Generating mpileup file using samtools
mpileup
samtools
updated 16 days ago by
Joe
21k • written 16 days ago by
Ruqaiya
• 0
3
votes
2
replies
201
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
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
4
replies
331
views
Truncated metadata file report from ENA Portal API
ena
python
9 days ago by
Giulia
• 0
3
votes
7
replies
422
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
20 days ago by
salias
• 0
3
votes
3
replies
294
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
2
votes
5
replies
547
views
Marking duplicates using UMIs
Deduplication
UMI
updated 27 days ago by
i.sudbery
19k • written 28 days ago by
Lipika
• 0
2
votes
5
replies
792
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 29 days ago by
Jesse
▴ 770 • written 4 weeks ago by
Ann
★ 2.4k
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
5 hours ago by
LauferVA
4.2k
2
votes
5
replies
958
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 20 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
2
replies
339
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 25 days ago by
Ram
43k • written 25 days ago by
v.berriosfarias
▴ 140
2
votes
2
replies
255
views
Raw counts using stringtie
stringtie
RNA-seq
updated 16 days ago by
GenoMax
142k • written 16 days ago by
ahmad.sajad4541
• 0
2
votes
4
replies
387
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
25 days ago by
samuelkalandarov2002
▴ 10
2
votes
3
replies
354
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 10 days ago by
bk11
★ 2.5k • written 14 days ago by
Yoosef
▴ 60
2
votes
2
replies
246
views
PDB related issue
rcsb
pdb
updated 20 days ago by
noodle
▴ 580 • written 21 days ago by
Nafi
• 0
2
votes
3
replies
334
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 16 days ago by
dthorbur
★ 2.0k • written 16 days ago by
Vijith
▴ 30
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
2
replies
260
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 15 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
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 16 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
1
vote
4
replies
507
views
cellranger error message
multiplexing
cellranger
updated 9 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
1
vote
4
replies
353
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
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 26 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
0
replies
197
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
24 days ago by
rohitsatyam102
▴ 870
1
vote
2
replies
258
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 19 days ago by
Ram
43k • written 19 days ago by
Ravita
• 0
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by
bef1
• 0
1
vote
4
replies
322
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
3
replies
384
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 21 days ago by
ATpoint
82k • written 21 days ago by
Francesco
▴ 10
1
vote
0
replies
143
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
10 days ago by
Shae
▴ 10
1
vote
2
replies
207
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
12 days ago by
robert.flynn.21
• 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
8
replies
559
views
Downsampling fastq file
downsample
fastq
19 days ago by
marco.barr
▴ 130
1
vote
0
replies
561
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
29 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
163
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 10 days ago by
andres.firrincieli
3.6k • written 10 days ago by
kacollier
▴ 30
1
vote
1
reply
257
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 18 days ago by
Ram
43k • written 19 days ago by
Jonathan Yoou
▴ 60
1
vote
3
replies
332
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 18 days ago by
GenoMax
142k • written 19 days ago by
jeffrey.maurer.informatics
• 0
1
vote
1
reply
187
views
student
epitranscriptomics
updated 12 days ago by
ATpoint
82k • written 12 days ago by
useriwa
• 0
1
vote
0
replies
178
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
10 days ago by
eebloom
▴ 80
1
vote
1
reply
271
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 24 days ago by
ATpoint
82k • written 24 days ago by
AaronJaime
• 0
1
vote
1
reply
199
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
1
reply
149
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
1
vote
1
reply
173
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
311 results • Page
1 of 7
Recent Votes
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
Answer: Duplicated sequence samtools
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161k
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to
Sara
▴ 30
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carlopecoraro2
★ 2.5k
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scideas
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Recent Replies
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
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?
by
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
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.
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