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86 results • Page
2 of 2
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0
votes
1
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74
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
6 hours ago by
asalimih
▴ 60
0
votes
1
reply
80
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 5 hours ago by
yura.grabovska
▴ 70 • written 6 hours ago by
ev97
▴ 20
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 0
0
votes
0
replies
160
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 5 days ago by
Ram
43k • written 5 days ago by
naomiboldon
• 0
0
votes
0
replies
38
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
180
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
0
votes
0
replies
117
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 6 days ago by
Ram
43k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
89
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
0
replies
167
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 5 days ago by
zx8754
11k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
154
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 days ago by
Samantha
• 0
0
votes
0
replies
142
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
0
votes
0
replies
99
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
0
replies
30
views
Add line under stat test
stats
R
2 hours ago by
Ghada
• 0
0
votes
0
replies
28
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
2 hours ago by
mgranada3
▴ 30
0
votes
0
replies
152
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
0
votes
0
replies
69
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
21 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
75
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 20 hours ago by
GenoMax
142k • written 21 hours ago by
Dude
• 0
1
vote
0
replies
138
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
6 days ago by
Shae
▴ 10
0
votes
0
replies
157
views
supervised admixture
supervised
admixture
6 days ago by
RT
▴ 10
0
votes
0
replies
63
views
ReactomeGSA
ReactomeGSA
14 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
187
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
6 days ago by
Matvii Mykhailichenko
• 0
1
vote
0
replies
176
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
6 days ago by
eebloom
▴ 80
0
votes
0
replies
12
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
33 minutes ago by
vk
▴ 10
0
votes
0
replies
53
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
8 hours ago by
Lélé
▴ 10
0
votes
0
replies
62
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 7 hours ago by
ATpoint
82k • written 8 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
52
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
6 hours ago by
jway
• 0
0
votes
0
replies
97
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
1
vote
0
replies
92
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
0
votes
0
replies
99
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
0
votes
0
replies
104
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
0
replies
7
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
20 minutes ago by
mavy
▴ 10
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
0
votes
0
replies
180
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
6 days ago by
Winter
• 0
0
votes
0
replies
115
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 2 days ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
105
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
86 results • Page
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
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Recent Replies
Comment: Inquiry about deseq2 transformation
by
Chen
• 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output
by
Brian Bushnell
20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools
by
kl
▴ 10
I corrected it. It shows the following which isn't exactly what I wanted. The second column I wanted to be the rsid extracted from the All_…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file
by
ramiro.barrantes
• 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation
by
Ram
43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
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by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
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I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
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Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
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MarcosCosta
• 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
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Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 120
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
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