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84 results • Page
1 of 2
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Views
Votes
Replies
0
votes
0
replies
19
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
1 hour ago by
mgranada3
▴ 30
0
votes
0
replies
24
views
Add line under stat test
stats
R
2 hours ago by
Ghada
• 0
0
votes
0
replies
35
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
Rodolfo Adrián
• 0
0
votes
1
reply
78
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 hours ago by
yura.grabovska
▴ 70 • written 5 hours ago by
ev97
▴ 20
0
votes
2
replies
88
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
4 hours ago by
hophuquy0944
• 0
0
votes
1
reply
73
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
5 hours ago by
asalimih
▴ 60
0
votes
0
replies
50
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
60
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 6 hours ago by
ATpoint
82k • written 7 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
52
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
3
replies
107
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
10 hours ago by
Esraa
• 0
0
votes
0
replies
61
views
ReactomeGSA
ReactomeGSA
13 hours ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
99
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 10 hours ago by
GenoMax
142k • written 15 hours ago by
chrisk
• 0
0
votes
1
reply
103
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 8 hours ago by
Joe
21k • written 17 hours ago by
iqra
• 0
0
votes
0
replies
74
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 19 hours ago by
GenoMax
142k • written 20 hours ago by
Dude
• 0
0
votes
0
replies
68
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
20 hours ago by
brunofelicianodeomena
• 0
0
votes
1
reply
121
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
17 hours ago by
sansan_96
▴ 90
0
votes
1
reply
141
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 1 day ago by
GenoMax
142k • written 1 day ago by
bioinfo
▴ 150
0
votes
2
replies
161
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
13 hours ago by
melissa.joubert
• 0
0
votes
0
replies
98
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
1
vote
1
reply
132
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
3
replies
191
views
How to access GWAVA software of data
GWAVA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
nonaddldy
▴ 10
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
2
replies
170
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
3
replies
331
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
155
views
How to process Bulk WES data?
WES
WGS
updated 2 days ago by
GenoMax
142k • written 2 days ago by
wyuan37
• 0
0
votes
1
reply
152
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 2 days ago by
cedric.blais
• 0
0
votes
1
reply
142
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 2 days ago by
Ram
43k • written 2 days ago by
eking28
• 0
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
0
votes
4
replies
241
views
Galaxy StringTie error
stringtie
galaxy
1 day ago by
trkfs
• 0
0
votes
0
replies
99
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
1
vote
4
replies
329
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 20 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
1
reply
154
views
consensus sequence calling
consensus
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
Ghada
• 0
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
0
replies
97
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
1
vote
0
replies
92
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
3
votes
2
replies
180
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 2 days ago by
ATpoint
82k • written 2 days ago by
jennyp0706
• 0
0
votes
0
replies
104
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
1
vote
2
replies
348
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 2 days ago by
Ram
43k • written 3 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
200
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
ramendra.sarma
• 0
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
0
votes
4
replies
384
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 days ago by
beginner123
• 0
0
votes
2
replies
224
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
2 days ago by
analyst
▴ 50
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
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
1
vote
3
replies
277
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 5 days ago by
Ram
43k • written 5 days ago by
Omics data mining
▴ 260
0
votes
5
replies
310
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
0
votes
1
reply
184
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
283
views
How are score_weights calculated in this code?
single-cell
4 days ago by
carolofharvest
▴ 40
0
votes
1
reply
217
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
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
84 results • Page
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Recent Votes
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
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Answer: Cannot install bwa-mem2 via conda
Answer: Cluster sub-set analysis using Seurat
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Recent Replies
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…
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. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat
by
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
★ 1.2k
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…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
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