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1,000 results • Page
1 of 20
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0
votes
0
replies
1
view
samtools write-index
samtools
just now by
LucisTheFather
• 0
0
votes
0
replies
12
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
40 minutes ago by
dlera.lozano
▴ 10
0
votes
0
replies
18
views
How to get 2 seurat objects into a DEseq
help
troubleshoot
1 hour ago by
He11oJe11o
• 0
0
votes
0
replies
45
views
DIFFBIND boxplot results, p value not significant
ChIP-seq
DiffBind
5 hours ago by
RD
▴ 10
0
votes
2
replies
121
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
5 hours ago by
ezz3
• 0
0
votes
4
replies
142
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
5 hours ago by
shpak.max
▴ 50
0
votes
1
reply
80
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
s
• 0
0
votes
2
replies
142
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
10 hours ago by
Shukai
• 0
0
votes
0
replies
62
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 12 hours ago by
GenoMax
142k • written 12 hours ago by
LuciaNhu
• 0
1
vote
2
replies
139
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 10 hours ago by
Ram
44k • written 12 hours ago by
Harshita
• 0
2
votes
0
replies
69
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 8 hours ago by
Ram
44k • written 13 hours ago by
Rafael Soler
★ 1.2k
0
votes
1
reply
98
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 13 hours ago by
DBScan
▴ 300 • written 14 hours ago by
brunomiwa
• 0
0
votes
0
replies
62
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
14 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
125
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 8 hours ago by
Ram
44k • written 14 hours ago by
pirku
• 0
0
votes
0
replies
65
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
18 hours ago by
Yao
▴ 30
0
votes
0
replies
70
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
19 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
202
views
Where to find old version of GATK best practice
gatk
10 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
96
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 20 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
Peter Chung
▴ 200
0
votes
1
reply
107
views
CreateSeuratObject taking very long
seurat
updated 15 hours ago by
Nitin Narwade
★ 1.6k • written 1 day ago by
eae6d2e7
• 0
0
votes
2
replies
177
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
14 hours ago by
Bjorn
• 0
0
votes
3
replies
230
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day ago by
marco.barr
▴ 130 • written 2 days ago by
Mohamed Samir
▴ 20
0
votes
1
reply
128
views
vcf phasing
beagle
WhatsHap
phasing
updated 15 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
0
replies
91
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
ev97
▴ 20
0
votes
1
reply
137
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
sooni
▴ 20
0
votes
1
reply
104
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
0
replies
81
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
1 day ago by
V_Vibes
• 0
0
votes
0
replies
149
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 1 day ago by
Ram
44k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
100
views
transcriptome annotation
annotation
trinity
transcriptome
updated 1 day ago by
Ram
44k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
225
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 1 day ago by
mnx0723
• 0
0
votes
1
reply
144
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 1 day ago by
zx8754
11k • written 2 days ago by
Ali
• 0
0
votes
4
replies
246
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 2 days ago by
sooni
▴ 20
0
votes
0
replies
100
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
2 days ago by
Maryam
• 0
0
votes
4
replies
332
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 days ago by
Bibi
• 0
0
votes
0
replies
112
views
handling bio replicates for chromHMM
replicates
chromHMM
2 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
104
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
2 days ago by
DGTool
▴ 20
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 1 day ago by
Ram
44k • written 2 days ago by
Rodolfo Adrián
• 0
1
vote
2
replies
381
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 9 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
139
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
145
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 0
0
votes
1
reply
187
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Jacek
▴ 20
0
votes
0
replies
149
views
How can i use ESM-1v ?
VEP
ESM-1v
4 days ago by
Meto
• 0
0
votes
0
replies
157
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Long
• 0
0
votes
0
replies
151
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
4 days ago by
kilcdincer
▴ 10
0
votes
0
replies
165
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
388
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 days ago by
dthorbur
★ 2.0k • written 5 days ago by
BATMAN
• 0
0
votes
6
replies
380
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
4 days ago by
hannes.bongartz
• 0
0
votes
0
replies
155
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 4 days ago by
GenoMax
142k • written 4 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
209
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
6
replies
358
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
16 hours ago by
Umer
▴ 50
0
votes
2
replies
261
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
melissachua90
▴ 70
1,000 results • Page
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GO analysis: Different results EnrichGO vs ShinyGO
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
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
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",…
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…
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