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116,002 results • Page
2 of 2321
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
97
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
97
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
0
votes
2
replies
213
views
Using the Ontology Lookup Service (OLS) API
API
OLS
19 hours ago by
longoka
▴ 40
7
votes
2
replies
195
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 1 day ago by
gconcepcion
▴ 410 • written 1 day ago by
eorr
▴ 30
2
votes
3
replies
233
views
Extracting information from my VCF file
VCF
updated 1 day ago by
bioruffo
▴ 40 • written 1 day ago by
realtreeecat
• 0
0
votes
3
replies
208
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
updated 16 hours ago by
LChart
3.9k • written 1 day ago by
rohitsatyam102
▴ 840
0
votes
2
replies
269
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 1 day ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
2
votes
3
replies
442
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 23 hours ago by
b.contreras.moreira
▴ 70 • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
89
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 1 day ago by
Ram
43k • written 1 day ago by
piotto
▴ 20
0
votes
2
replies
184
views
Fpkm and log2fold change and pcr validation
fpkm
updated 1 day ago by
bioruffo
▴ 40 • written 1 day ago by
mounavisirekolam
• 0
2
votes
2
replies
199
views
Location of NCBI ftp site changed?
ftp
ncbi
1 day ago by
sampsa.hyvamaki
• 0
0
votes
1
reply
161
views
MACS3 or SEACR
MACS3
SEACR
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
daffodil
▴ 10
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 1 day ago by
GenoMax
140k • written 1 day ago by
houssi301
• 0
0
votes
0
replies
94
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
1 day ago by
Adrian Pelin
★ 2.6k
1
vote
1
reply
151
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 1 day ago by
dthorbur
★ 1.7k • written 1 day ago by
andrebolerbarros
• 0
0
votes
1
reply
145
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
Mary
• 0
0
votes
1
reply
219
views
What alternative method would recommend for conducting gene ontology analysis?
WEGO
gene-ontology
updated 1 day ago by
dthorbur
★ 1.7k • written 2 days ago by
mathavanbioinfo
▴ 80
1
vote
6
replies
332
views
Nanopore data filtering using fastp
fastp
nanopore
15 minutes ago by
emilydolivo97
• 0
1
vote
2
replies
215
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
2
votes
2
replies
222
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
3
votes
12
replies
620
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
23 hours ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
144
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 1 day ago by
zx8754
11k • written 2 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
0
replies
105
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
1
vote
2
replies
226
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
1
vote
0
replies
93
views
Job:
Job Opening - Fred Hutch - Director of Training & Community
fred-hutchinson
updated 1 day ago by
Ram
43k • written 2 days ago by
Fred Hutch (Recruiting)
▴ 20
0
votes
0
replies
106
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
2 days ago by
Yingying
• 0
0
votes
0
replies
103
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
PBC
▴ 10
0
votes
3
replies
237
views
Parsing fasta file by coordinates
linux
fasta
updated 2 days ago by
GenoMax
140k • written 2 days ago by
sorrymouse
▴ 120
0
votes
2
replies
214
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
1 day ago by
eesiribloom
▴ 50
0
votes
2
replies
200
views
Using velocyto on 3'UTR 10x single-cell RNA-Seq data
single-cell
single-end
10x
velocyto
1 day ago by
Sergio
• 0
0
votes
0
replies
117
views
Job:
Post-doctoral positions in computational biomedicine
data-science
biomedicine
machine-learning
updated 2 days ago by
Ram
43k • written 2 days ago by
pandey.gaurav
▴ 200
6
votes
13
replies
466
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
2 days ago by
Maverick
▴ 10
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 1 day ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
0
votes
5
replies
452
views
How to download RNAseq data of only male KIRC patients?
TCGAbiolinks
2 days ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
84
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
2 days ago by
erbrocato
• 0
0
votes
1
reply
126
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
0
replies
101
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
barrypraveen
▴ 130
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 2 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
0
votes
3
replies
221
views
What tools to assess coverage, completeness and contamination?
completeness
contamination
covarage
updated 2 days ago by
Mensur Dlakic
★ 26k • written 2 days ago by
Kárita
• 0
0
votes
0
replies
80
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 2 days ago by
Ram
43k • written 2 days ago by
La52dA97b6
• 0
4
votes
9
replies
663
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 2 days ago by
Simon
▴ 10 • written 6 days ago by
Maxwell
▴ 20
0
votes
1
reply
163
views
RNA-seq with normalized cpm count
RNA-seq
Deseq2
EdgeR
updated 2 days ago by
Ram
43k • written 2 days ago by
GiV17
▴ 50
0
votes
2
replies
197
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 2 days ago by
Ram
43k • written 2 days ago by
Bioinfonext
▴ 460
0
votes
4
replies
250
views
Confirm if a genome position falls into a coding exon
exon
UCSC
coding
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
Lila M
★ 1.2k
1
vote
0
replies
96
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
2 days ago by
mrazib0210
▴ 10
0
votes
1
reply
144
views
NCBI gene data
Variants
NCBI
updated 2 days ago by
GenoMax
140k • written 2 days ago by
chandrakala.m
• 0
0
votes
1
reply
138
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 2 days ago by
Ram
43k • written 2 days ago by
Sony
▴ 10
3
votes
0
replies
119
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
2 days ago by
Biostar
2.6k
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 2 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
116,002 results • Page
2 of 2321
Recent Votes
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
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Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
Comment: Variant calling of GBS data
by
analyst
▴ 10
Vcf file contains this information ![enter image description here][1] [1]: /media/images/b3f699e5-2dd9-4e08-8f5b-2a716544
Comment: Variant calling of GBS data
by
analyst
▴ 10
Command used : **java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --filter-name "QD_f…
Comment: Variant calling of GBS data
by
analyst
▴ 10
I am using gatK version 4.2.1.0 for variant filtration but it generates following warnings: 14:10:40.970 WARN JexlEngine - ![0,14]: 'Read…
Comment: STAR aligner options
by
dsull
★ 5.6k
In that first link, Dr. Dobin states how such configurations will "split" the reads into pieces -- exactly what I alluded to in my comment.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you for this advice , but when reading the documentation of split2 I found that it generates multiple files for the same fastq file. …
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
ATpoint
81k
I will delete this as it - obviously - does not belong into this thread.
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
• 0
you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
• 0
Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
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