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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
358
views
Merge clusters in Seurat UMAP
seurat
umap
4 days ago by
kilcdincer
▴ 10
0
votes
0
replies
161
views
Use of ichor CNA
Dog
CNA
genome
5 days ago by
sainavyav22
• 0
2
votes
2
replies
291
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 5 days ago by
Ram
44k • written 5 days ago by
txema.heredia
▴ 130
0
votes
0
replies
163
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
5 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
268
views
How can I calculate the OS of each patient?
overall-survival
1 day ago by
Pedro
• 0
0
votes
0
replies
155
views
cat-bgen fail
bgenix
updated 5 days ago by
Ram
44k • written 5 days ago by
lambard
• 0
1
vote
1
reply
211
views
API kegg - IndexError: list index out of range
kegg
API
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
149
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
5 days ago by
ebertomeup
• 0
0
votes
3
replies
294
views
Sam file Header problem
Sam
Header
problem
file
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
saifulislam99121
• 0
0
votes
0
replies
151
views
select set of intervals that cover a genomic region
GRanges
bed
5 days ago by
ntsopoul
▴ 60
0
votes
3
replies
237
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 1 hour ago by
Nyksubuz
▴ 20 • written 5 days ago by
Luqman
• 0
0
votes
5
replies
349
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
1
reply
184
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 5 days ago by
Michael
54k • written 6 days ago by
mgranada3
▴ 30
0
votes
1
reply
169
views
Add line under stat test
stats
R
updated 4 days ago by
Nyksubuz
▴ 20 • written 6 days ago by
Ghada
• 0
0
votes
0
replies
117
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Rodolfo Adrián
• 0
1
vote
16
replies
791
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 3 days ago by
GenoMax
142k • written 6 days ago by
hophuquy0944
• 0
0
votes
1
reply
146
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
6 days ago by
asalimih
▴ 60
0
votes
0
replies
117
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
6 days ago by
jway
• 0
0
votes
1
reply
166
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 days ago by
Papyrus
★ 2.9k • written 6 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
161
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 5 days ago by
GenoMax
142k • written 6 days ago by
Lélé
▴ 10
0
votes
3
replies
185
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
6 days ago by
Esraa
• 0
0
votes
0
replies
101
views
ReactomeGSA
ReactomeGSA
6 days ago by
Shaimaa Gamal
▴ 10
0
votes
5
replies
303
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 6 days ago by
GenoMax
142k • written 6 days ago by
chrisk
• 0
0
votes
1
reply
186
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 5 days ago by
DGTool
▴ 20 • written 6 days ago by
iqra
• 0
0
votes
0
replies
105
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Dude
• 0
0
votes
0
replies
101
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
7 days ago by
brunofelicianodeomena
• 0
0
votes
1
reply
154
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
6 days ago by
sansan_96
▴ 90
2
votes
2
replies
250
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
5 days ago by
bioinfo
▴ 150
0
votes
2
replies
210
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 days ago by
melissa.joubert
• 0
0
votes
0
replies
117
views
Is there a real ground truth for CNV data?
CNV
7 days ago by
jennyp0706
• 0
1
vote
1
reply
153
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 7 days ago by
Ram
44k • written 7 days ago by
kilcdincer
▴ 10
0
votes
3
replies
219
views
How to access GWAVA software of data
GWAVA
updated 7 days ago by
GenoMax
142k • written 7 days ago by
nonaddldy
▴ 10
0
votes
0
replies
98
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
7 days ago by
Spring
• 0
0
votes
2
replies
200
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
7 days ago by
IdaHao0921
• 0
0
votes
3
replies
362
views
Snakemake wrapper issue
fastqc
snakemake
updated 7 days ago by
Wei-Chen Pan
• 0 • written 10 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
170
views
How to process Bulk WES data?
WES
WGS
updated 8 days ago by
GenoMax
142k • written 8 days ago by
wyuan37
• 0
0
votes
1
reply
165
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 8 days ago by
GenoMax
142k • written 8 days ago by
cedric.blais
• 0
0
votes
1
reply
155
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 8 days ago by
Ram
44k • written 8 days ago by
eking28
• 0
0
votes
0
replies
108
views
reference-free assembly error assessment tools
assembly
8 days ago by
lagartija
▴ 160
0
votes
4
replies
274
views
Galaxy StringTie error
stringtie
galaxy
7 days ago by
trkfs
• 0
0
votes
0
replies
107
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
8 days ago by
atariw
▴ 10
1
vote
4
replies
362
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 7 days ago by
Juke34
8.6k • written 8 days ago by
Vijith
▴ 30
0
votes
1
reply
168
views
consensus sequence calling
consensus
updated 8 days ago by
bk11
★ 2.5k • written 8 days ago by
Ghada
• 0
0
votes
0
replies
92
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
8 days ago by
JACKY
▴ 140
0
votes
0
replies
107
views
Reference panel of normals for ensembl named refgenome
Mutect2
8 days ago by
gernophil
▴ 80
1
vote
0
replies
101
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
8 days ago by
tomas4482
▴ 400
3
votes
2
replies
208
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 8 days ago by
ATpoint
82k • written 8 days ago by
jennyp0706
• 0
0
votes
0
replies
116
views
lncRNA
tcga
lncrna
8 days ago by
jain72744
▴ 10
1
vote
2
replies
377
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 8 days ago by
Ram
44k • written 9 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
221
views
Output file of samtools flagstat empty
samtools-flagstat
updated 8 days ago by
colindaven
6.4k • written 9 days ago by
ramendra.sarma
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
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