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87 results • Page
2 of 2
Sort: Votes
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Votes
Replies
0
votes
0
replies
70
views
ReactomeGSA
ReactomeGSA
18 hours ago by
Shaimaa Gamal
▴ 10
0
votes
3
replies
118
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
16 hours ago by
Esraa
• 0
0
votes
1
reply
110
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 13 hours ago by
Joe
21k • written 22 hours ago by
iqra
• 0
0
votes
0
replies
62
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
13 hours ago by
Lélé
▴ 10
0
votes
0
replies
70
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 12 hours ago by
ATpoint
82k • written 13 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
59
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
11 hours ago by
jway
• 0
0
votes
1
reply
84
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
10 hours ago by
asalimih
▴ 60
0
votes
1
reply
94
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 10 hours ago by
yura.grabovska
▴ 70 • written 10 hours ago by
ev97
▴ 20
0
votes
2
replies
106
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
9 hours ago by
hophuquy0944
• 0
0
votes
0
replies
49
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
47
views
Add line under stat test
stats
R
7 hours ago by
Ghada
• 0
0
votes
0
replies
48
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
7 hours ago by
mgranada3
▴ 30
0
votes
9
replies
581
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
5 hours ago by
Arton
▴ 10
0
votes
0
replies
32
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
4 hours ago by
mavy
▴ 10
0
votes
5
replies
195
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 hour ago by
GenoMax
142k • written 20 hours ago by
chrisk
• 0
0
votes
1
reply
50
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
updated 1 hour ago by
GenoMax
142k • written 4 hours ago by
vk
▴ 10
0
votes
0
replies
13
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
1 hour ago by
sooni
▴ 20
0
votes
0
replies
7
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
40 minutes ago by
Luqman
• 0
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
107
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 0
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
0
votes
1
reply
152
views
input file for alternative splicing in rmats in linux
rmats
updated 6 days ago by
Ram
43k • written 6 days ago by
Lambodarswain316
• 0
0
votes
0
replies
157
views
supervised admixture
supervised
admixture
6 days ago by
RT
▴ 10
0
votes
0
replies
153
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
6 days ago by
Aytaç
• 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
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
2
replies
225
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
5 days ago by
jain72744
▴ 10
0
votes
1
reply
213
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Amr
▴ 160
0
votes
1
reply
189
views
Microbial Signal Transduction Database
MiST
updated 5 days ago by
zx8754
11k • written 5 days ago by
Shravani
• 0
0
votes
0
replies
168
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
1
reply
185
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 5 days ago by
GenoMax
142k • written 5 days ago by
maria.soler
• 0
0
votes
2
replies
268
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 12 days ago by
Ximena
• 0
0
votes
1
reply
218
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 5 days ago by
curious
▴ 750 • written 5 days ago by
SeoGyun
• 0
0
votes
2
replies
224
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 5 days ago by
Ram
43k • written 6 days ago by
sainavyav22
• 0
0
votes
1
reply
199
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 5 days ago by
Ram
43k • written 5 days ago by
Shwetha
• 0
0
votes
0
replies
162
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
4
replies
297
views
Correlation Analysis
statistics
methylation
NGS
expression
4 days ago by
Researcher
▴ 30
87 results • Page
2 of 2
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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Scholar
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ramiro.barrantes
• 0
Popular Question
to
AshleeThomson
▴ 80
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vk
▴ 10
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27k
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Recent Replies
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
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
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
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…
Comment: Filtering VCF files based on VAF giving incorrect results
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…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
by
Ash
▴ 10
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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