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312 results • Page
1 of 7
Sort: Votes
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Votes
Replies
5
votes
5
replies
347
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
516
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 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
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
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
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 10 days ago by
Eren
• 0
3
votes
4
replies
332
views
Truncated metadata file report from ENA Portal API
ena
python
9 days ago by
Giulia
• 0
3
votes
3
replies
295
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
3
votes
2
replies
203
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
8
replies
637
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
13 days ago by
Qroid
▴ 40
3
votes
3
replies
560
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
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
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
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
2
votes
5
replies
547
views
Marking duplicates using UMIs
Deduplication
UMI
updated 27 days ago by
i.sudbery
19k • written 29 days ago by
Lipika
• 0
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
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
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
5
replies
798
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
946
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 26 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 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
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
248
views
PDB related issue
rcsb
pdb
updated 21 days ago by
noodle
▴ 580 • written 21 days ago by
Nafi
• 0
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
11 hours ago by
LauferVA
4.2k
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 26 days ago by
v.berriosfarias
▴ 140
2
votes
2
replies
266
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
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
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
3
replies
283
views
STAR aligner error
RNA-seq
STAR
slurm
updated 11 days ago by
Ram
43k • written 12 days ago by
M.
▴ 30
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 22 days ago by
Francesco
▴ 10
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
24 days ago by
ahmad.sajad4541
• 0
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
3
replies
343
views
some error in building kraken2 database
metagenome
kraken2
26 days ago by
Art1ess
• 0
1
vote
2
replies
283
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
★ 7.2k • written 5 weeks ago by
Netanel
• 0
1
vote
2
replies
210
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
12 days ago by
robert.flynn.21
• 0
1
vote
6
replies
418
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 16 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
1
vote
2
replies
259
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
8
replies
559
views
Downsampling fastq file
downsample
fastq
19 days ago by
marco.barr
▴ 130
1
vote
0
replies
99
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
6 days ago by
tomas4482
▴ 400
1
vote
3
replies
456
views
PCA plot
DESeq2
PCAplot
updated 21 days ago by
LauferVA
4.2k • written 24 days ago by
Aaliya
▴ 10
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by
bef1
• 0
1
vote
1
reply
258
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 19 days ago by
Ram
43k • written 19 days ago by
Jonathan Yoou
▴ 60
1
vote
4
replies
327
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 11 days ago by
cput
• 0
1
vote
9
replies
437
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 9 days ago by
i.sudbery
19k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
332
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 19 days ago by
GenoMax
142k • written 19 days ago by
jeffrey.maurer.informatics
• 0
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
1
reply
200
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
188
views
student
epitranscriptomics
updated 12 days ago by
ATpoint
82k • written 12 days ago by
useriwa
• 0
1
vote
1
reply
459
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 10 days ago by
Jaïr
• 0 • written 5 months ago by
NorbertK
▴ 10
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
312 results • Page
1 of 7
Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
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
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Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: 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…
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