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111 results • Page
2 of 3
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
77
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
0
votes
1
reply
140
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
0
replies
69
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
0
votes
0
replies
84
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
0
votes
0
replies
70
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
0
votes
0
replies
78
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
3 days ago by
Biostars2200
• 0
0
votes
0
replies
124
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
Atul K.
• 0
2
votes
5
replies
433
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
0
replies
137
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
132
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
4 days ago by
Mamatha Y S
• 0
0
votes
2
replies
257
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
537
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
5 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
210
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
4 days ago by
abhishekghadge
• 0
2
votes
5
replies
680
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
0
votes
0
replies
185
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 5 days ago by
Ram
43k • written 5 days ago by
mja
• 0
0
votes
0
replies
186
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
5 days ago by
Nitin
• 0
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Ram
43k • written 5 days ago by
yifangt86
▴ 60
0
votes
0
replies
180
views
Chemical structure validation
structure
cap
validation
metabolite
5 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation
genomics
updated 5 days ago by
Ram
43k • written 5 days ago by
Emmi
• 0
0
votes
0
replies
176
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
5 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
280
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
0
votes
0
replies
193
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 5 days ago by
Ram
43k • written 6 days ago by
Dinmukhamed
• 0
0
votes
0
replies
192
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by
Atul K.
• 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by
Ram
43k • written 6 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
464
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
0
votes
2
replies
533
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
0
votes
0
replies
211
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 6 days ago by
Ram
43k • written 6 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
419
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
2 days ago by
Javier
• 0
0
votes
0
replies
175
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
6 days ago by
enferdeflame
• 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Chris
▴ 260
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 6 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
157
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 6 days ago by
Ram
43k • written 7 days ago by
bioinfo223
▴ 10
1
vote
1
reply
391
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
0
votes
4
replies
574
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 days ago by
Kai Xin
• 0
2
votes
7
replies
810
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
1
vote
2
replies
228
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 17 days ago by
Netanel
• 0
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
2
replies
537
views
autodockvina
python
python3
autodock
updated 6 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 2 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
0
replies
731
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
1
reply
818
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 6 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 6 days ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 6 days ago by
Ram
43k • written 5.5 years ago by
baldissera152
▴ 10
111 results • Page
2 of 3
Recent Votes
Comment: SRA to BAM
Answer: What Is A "Spot" In Sra Format
Comment: Why gatk VariantAnnotator required bam and coverage files
Comment: Why gatk VariantAnnotator required bam and coverage files
discoSnp - reference-free finding of isolated SNPs from non assembled reads
Comment: Figures are disappeared from html report of SnpEff
Answer: Figures are disappeared from html report of SnpEff
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Recent Awards •
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Popular Question
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William
★ 5.3k
Scholar
to
Adrian Altenhoff
★ 1.1k
Popular Question
to
maxime.policarpo
▴ 200
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Hamtaro
▴ 50
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Nicolas Rosewick
11k
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★ 1.8k
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Keem Uarren Eiryll
• 0
Recent Replies
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
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