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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
25
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
2 hours ago by
Spring
• 0
0
votes
1
reply
37
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
updated 1 hour ago by
Pierre Lindenbaum
161k • written 3 hours ago by
IdaHao0921
• 0
0
votes
0
replies
47
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
5 hours ago by
Holly
• 0
0
votes
0
replies
48
views
Biomart issue, why so few 3'utrs?
utr
biomart
9 hours ago by
RNAseqer
▴ 270
0
votes
1
reply
100
views
How to process Bulk WES data?
WES
WGS
updated 11 hours ago by
GenoMax
142k • written 11 hours ago by
wyuan37
• 0
0
votes
1
reply
103
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 9 hours ago by
GenoMax
142k • written 12 hours ago by
cedric.blais
• 0
0
votes
1
reply
88
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 11 hours ago by
Ram
43k • written 13 hours ago by
eking28
• 0
0
votes
0
replies
61
views
reference-free assembly error assessment tools
assembly
16 hours ago by
lagartija
▴ 160
1
vote
0
replies
63
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
16 hours ago by
J.
▴ 10
0
votes
3
replies
146
views
Galaxy StringTie error
stringtie
galaxy
updated 9 hours ago by
Mathew
▴ 130 • written 17 hours ago by
trkfs
• 0
0
votes
0
replies
65
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
19 hours ago by
atariw
▴ 10
1
vote
3
replies
124
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
47 minutes ago by
Vijith
▴ 30
0
votes
1
reply
112
views
consensus sequence calling
consensus
updated 17 hours ago by
bk11
★ 2.4k • written 21 hours ago by
Ghada
• 0
0
votes
0
replies
62
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
21 hours ago by
JACKY
▴ 140
0
votes
0
replies
74
views
Reference panel of normals for ensembl named refgenome
Mutect2
23 hours ago by
gernophil
▴ 80
1
vote
0
replies
72
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
23 hours ago by
tomas4482
▴ 400
3
votes
2
replies
147
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
0
replies
89
views
lncRNA
tcga
lncrna
1 day ago by
jain72744
▴ 10
1
vote
2
replies
315
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 17 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
0
votes
2
replies
187
views
Output file of samtools flagstat empty
samtools-flagstat
updated 23 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
0
votes
0
replies
99
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
1 day ago by
BioinfGuru
★ 1.7k
0
votes
4
replies
356
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 day ago by
beginner123
• 0
0
votes
2
replies
209
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 day ago by
analyst
▴ 50
0
votes
1
reply
190
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 3 days ago by
Ram
43k • written 3 days ago by
Shwetha
• 0
0
votes
0
replies
158
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 3 days ago by
Ram
43k • written 3 days ago by
naomiboldon
• 0
1
vote
3
replies
267
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 3 days ago by
Ram
43k • written 3 days ago by
Omics data mining
▴ 260
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
19 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
177
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 3 days ago by
GenoMax
142k • written 3 days ago by
maria.soler
• 0
0
votes
2
replies
268
views
How are score_weights calculated in this code?
single-cell
2 days ago by
carolofharvest
▴ 40
0
votes
1
reply
210
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 3 days ago by
curious
▴ 750 • written 3 days ago by
SeoGyun
• 0
0
votes
0
replies
149
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 days ago by
Samantha
• 0
0
votes
1
reply
180
views
Microbial Signal Transduction Database
MiST
updated 4 days ago by
zx8754
11k • written 4 days ago by
Shravani
• 0
0
votes
0
replies
137
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
4 days ago by
singcell
• 0
0
votes
1
reply
204
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Amr
▴ 160
0
votes
2
replies
216
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
4 days ago by
jain72744
▴ 10
3
votes
1
reply
193
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 3 days ago by
dthorbur
★ 2.0k • written 4 days ago by
Eren
• 0
0
votes
0
replies
147
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
4 days ago by
Aytaç
• 0
0
votes
0
replies
164
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 4 days ago by
zx8754
11k • written 4 days ago by
curious_butterfly
• 0
0
votes
0
replies
154
views
supervised admixture
supervised
admixture
4 days ago by
RT
▴ 10
0
votes
2
replies
214
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 3 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
3
votes
4
replies
300
views
Truncated metadata file report from ENA Portal API
ena
python
3 days ago by
Giulia
• 0
0
votes
0
replies
180
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
4 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
144
views
input file for alternative splicing in rmats in linux
rmats
updated 4 days ago by
Ram
43k • written 4 days ago by
Lambodarswain316
• 0
1
vote
1
reply
441
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 4 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
0
replies
131
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
4 days ago by
Shae
▴ 10
1
vote
1
reply
150
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 5 days ago by
andres.firrincieli
3.6k • written 5 days ago by
kacollier
▴ 30
0
votes
0
replies
113
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 5 days ago by
Ram
43k • written 5 days ago by
curious_butterfly
• 0
1
vote
3
replies
240
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 4 days ago by
GenoMax
142k • written 5 days ago by
cput
• 0
0
votes
0
replies
115
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
5 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 5 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
1,000 results • Page
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Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
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Recent Replies
Answer: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment
by
ATpoint
82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
by
ATpoint
82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data
by
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82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare?
by
ATpoint
82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
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161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue
by
Matvii Mykhailichenko
• 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ?
by
marco.barr
▴ 110
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
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by
Wei-Chen Pan
• 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results?
by
林明德
• 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
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by
Ashfaq
• 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
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