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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
413
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 days ago by
beginner123
• 0
0
votes
2
replies
238
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
8 days ago by
analyst
▴ 50
0
votes
1
reply
209
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 10 days ago by
Ram
43k • written 10 days ago by
Shwetha
• 0
0
votes
0
replies
171
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 10 days ago by
Ram
44k • written 11 days ago by
naomiboldon
• 0
3
votes
3
replies
320
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 10 days ago by
Ram
43k • written 11 days ago by
Omics data mining
▴ 260
0
votes
5
replies
353
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
8 days ago by
SilhouetteQ
• 0
0
votes
1
reply
214
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 11 days ago by
GenoMax
142k • written 11 days ago by
maria.soler
• 0
0
votes
2
replies
306
views
How are score_weights calculated in this code?
single-cell
10 days ago by
carolofharvest
▴ 40
0
votes
1
reply
235
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 10 days ago by
curious
▴ 750 • written 11 days ago by
SeoGyun
• 0
0
votes
0
replies
161
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
11 days ago by
Samantha
• 0
0
votes
1
reply
203
views
Microbial Signal Transduction Database
MiST
updated 11 days ago by
zx8754
11k • written 11 days ago by
Shravani
• 0
0
votes
0
replies
151
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
11 days ago by
singcell
• 0
0
votes
1
reply
231
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 11 days ago by
ATpoint
82k • written 11 days ago by
Amr
▴ 160
0
votes
2
replies
256
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
11 days ago by
jain72744
▴ 10
3
votes
1
reply
219
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 11 days ago by
dthorbur
★ 2.0k • written 11 days ago by
Eren
• 0
0
votes
0
replies
162
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
11 days ago by
Aytaç
• 0
0
votes
0
replies
176
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 11 days ago by
zx8754
11k • written 11 days ago by
curious_butterfly
• 0
0
votes
0
replies
170
views
supervised admixture
supervised
admixture
11 days ago by
RT
▴ 10
0
votes
2
replies
244
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 10 days ago by
Ram
43k • written 11 days ago by
sainavyav22
• 0
3
votes
4
replies
353
views
Truncated metadata file report from ENA Portal API
ena
python
10 days ago by
Giulia
• 0
0
votes
0
replies
194
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
12 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
167
views
input file for alternative splicing in rmats in linux
rmats
updated 12 days ago by
Ram
43k • written 12 days ago by
Lambodarswain316
• 0
1
vote
1
reply
468
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 12 days ago by
Jaïr
• 0 • written 5 months ago by
NorbertK
▴ 10
1
vote
0
replies
152
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
12 days ago by
Shae
▴ 10
1
vote
1
reply
174
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 12 days ago by
andres.firrincieli
3.6k • written 12 days ago by
kacollier
▴ 30
0
votes
0
replies
126
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 12 days ago by
Ram
43k • written 12 days ago by
curious_butterfly
• 0
1
vote
4
replies
347
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
Joe
21k • written 12 days ago by
cput
• 0
0
votes
0
replies
128
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
12 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 12 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
0
replies
117
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 12 days ago by
Ram
43k • written 12 days ago by
mathavanbioinfo
▴ 90
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 13 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
5
votes
7
replies
534
views
RNA seq analysis
DESeq
RNA-seq
6 days ago by
Jacek
▴ 20
0
votes
0
replies
153
views
Chance for trained without experience
bio
updated 13 days ago by
ATpoint
82k • written 13 days ago by
shehab
• 0
0
votes
0
replies
136
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
13 days ago by
Omics data mining
▴ 260
0
votes
2
replies
210
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
13 days ago by
njornet
▴ 20
0
votes
2
replies
237
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 12 days ago by
Adam
▴ 30 • written 13 days ago by
Darya
• 0
0
votes
5
replies
316
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 13 days ago by
Joe
21k • written 13 days ago by
Lemonhope
• 0
0
votes
0
replies
191
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
12 days ago by
Winter
• 0
0
votes
0
replies
113
views
meffil.snp.concordance
meffil
methylation
snp_concordance
13 days ago by
kyj222637
• 0
0
votes
1
reply
175
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 13 days ago by
Bastien Hervé
5.3k • written 13 days ago by
sooni
▴ 20
1
vote
3
replies
286
views
STAR aligner error
RNA-seq
STAR
slurm
updated 12 days ago by
Ram
44k • written 13 days ago by
M.
▴ 30
0
votes
0
replies
107
views
monocle 3-- Could not get node in small cluster
monocle3
13 days ago by
synat.keam
▴ 100
0
votes
2
replies
235
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
13 days ago by
Nicholas
• 0
0
votes
1
reply
282
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 14 days ago by
GenoMax
142k • written 14 days ago by
Sony
▴ 10
5
votes
5
replies
354
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
13 days ago by
Chris
▴ 280
0
votes
2
replies
252
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 12 days ago by
swbarnes2
14k • written 14 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
461
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 11 days ago by
i.sudbery
19k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
191
views
student
epitranscriptomics
updated 14 days ago by
ATpoint
82k • written 14 days ago by
useriwa
• 0
0
votes
3
replies
221
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 14 days ago by
GenoMax
142k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
334
views
Correlation Analysis
statistics
methylation
NGS
expression
10 days ago by
Researcher
▴ 30
1,000 results • Page
3 of 20
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Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
A: How To Convert List Of Entrez Ids Into Gene Name
How To Convert List Of Entrez Ids Into Gene Name
A: RSeQC Output from infer_experiment.py - what does it mean?
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Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 220
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
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