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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
82
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
7 days ago by
alifafiq1
• 0
0
votes
0
replies
87
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
8 days ago by
feather-W
• 0
2
votes
4
replies
301
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
6 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
87
views
Annotating single cell data automatically
cell
annotation
single
8 days ago by
Gerard
• 0
0
votes
1
reply
163
views
RNA-seq bacteria contamination
RNA-seq
updated 8 days ago by
GenoMax
141k • written 8 days ago by
sh
• 0
0
votes
0
replies
77
views
Imputation advice
imputation
8 days ago by
kl
▴ 10
0
votes
0
replies
96
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
8 days ago by
Enrique
• 0
0
votes
0
replies
79
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
8 days ago by
sativus
▴ 20
0
votes
0
replies
86
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
8 days ago by
Biostars2200
• 0
0
votes
0
replies
136
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 8 days ago by
Carlo Yague
8.7k • written 8 days ago by
Atul K.
• 0
2
votes
5
replies
473
views
Marking duplicates using UMIs
Deduplication
UMI
updated 8 days ago by
i.sudbery
19k • written 9 days ago by
Lipika
• 0
0
votes
0
replies
143
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 9 days ago by
Ram
43k • written 9 days ago by
sainavyav22
• 0
0
votes
0
replies
144
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
9 days ago by
rthapa
▴ 90
0
votes
0
replies
139
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
9 days ago by
Mamatha Y S
• 0
0
votes
2
replies
278
views
bam merging for archaic samples
samtools
bam
updated 9 days ago by
Ram
43k • written 10 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
544
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
10 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
220
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
10 days ago by
abhishekghadge
• 0
2
votes
5
replies
707
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 10 days ago by
Jesse
▴ 740 • written 11 days ago by
Ann
★ 2.4k
0
votes
0
replies
192
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 11 days ago by
Ram
43k • written 11 days ago by
mja
• 0
0
votes
0
replies
192
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
11 days ago by
Nitin
• 0
0
votes
0
replies
186
views
Chemical structure validation
structure
cap
validation
metabolite
11 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
270
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 11 days ago by
GenoMax
141k • written 11 days ago by
bioyas
▴ 10
0
votes
0
replies
210
views
Copy number variation plot
Copy-number-variation
genomics
updated 11 days ago by
Ram
43k • written 11 days ago by
Emmi
• 0
0
votes
0
replies
186
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
11 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
289
views
Could you please assist in identifying this cluster?
single-cell
updated 11 days ago by
Ram
43k • written 11 days ago by
Kazo
▴ 10
0
votes
0
replies
203
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 11 days ago by
Ram
43k • written 11 days ago by
Dinmukhamed
• 0
0
votes
0
replies
199
views
miRDeep2: How to get the read counts
mirdeep2
11 days ago by
Atul K.
• 0
0
votes
0
replies
204
views
Lncipedia GTF file error
Proteomics
updated 11 days ago by
Ram
43k • written 11 days ago by
atharvakarkare14
▴ 20
3
votes
3
replies
484
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 10 days ago by
swbarnes2
14k • written 11 days ago by
noodle
▴ 580
0
votes
2
replies
555
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
11 days ago by
航太郎
• 0
0
votes
0
replies
216
views
create genewise sync file in popoolation
popoolation
updated 12 days ago by
GenoMax
141k • written 12 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
385
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
11 days ago by
Ashok
• 0
0
votes
2
replies
420
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
11 days ago by
Ashok
• 0
0
votes
0
replies
218
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 12 days ago by
Ram
43k • written 12 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
428
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
11 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
209
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
8 days ago by
Javier
• 0
0
votes
0
replies
182
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
12 days ago by
enferdeflame
• 0
1
vote
1
reply
425
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 9 days ago by
Gordon Smyth
★ 7.1k • written 12 days ago by
Chris
▴ 260
0
votes
1
reply
404
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 12 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
161
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 12 days ago by
Ram
43k • written 12 days ago by
bioinfo223
▴ 10
0
votes
0
replies
181
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
12 days ago by
P.
• 0
0
votes
0
replies
172
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
12 days ago by
ekirsch
• 0
1
vote
1
reply
433
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
11 days ago by
renan.igor
• 0
0
votes
0
replies
185
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
12 days ago by
synat.keam
▴ 100
0
votes
1
reply
283
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 13 days ago by
GenoMax
141k • written 13 days ago by
ycts
• 0
0
votes
4
replies
600
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
11 days ago by
Kai Xin
• 0
1
vote
1
reply
236
views
Retrieve a % coverage for each transcript
RNA-seq
updated 13 days ago by
Ram
43k • written 13 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
389
views
How can I solve this error?
metal
12 days ago by
22211020193
• 0
0
votes
0
replies
175
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 13 days ago by
GenoMax
141k • written 13 days ago by
srimmer
• 0
1
vote
2
replies
294
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 13 days ago by
Ram
43k • written 13 days ago by
aniigodwinn
• 0
1,000 results • Page
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Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
Extracting genomic feature sequences from GTF/GFF files with AGAT
C: Problem with Ensembl version identifiers after running DESeq2
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Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
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▴ 310
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
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> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
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by
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43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 310
- p.adjust() is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, as…
Comment: Downsampling fastq file
by
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I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
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▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
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▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
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No it does not. Do you know of a way that can help me achieve what I want?
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UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
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thank you for your comment, but yes running DESeq2 is the starting point. dds <- DESeqDataSetFromMatrix(countData=RawCounts, …
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Please stop pasting a sentence in the `tags` field. That field is for subject matter keywords. I've fixed your posts this time, please be m…
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