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120,919 results • Page
1 of 2419
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0
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0
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1
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Getting sequences fragments using pysam
sequencing
pysam
reads
wgs
just now by
Julieta
• 0
4
votes
9
replies
2.9k
views
Does EnhancedVolcano() supports crosstalk()?
EnhancedVolcano
crosstalk
R
ggplot
updated 10 minutes ago by
Mauws
• 0 • written 5.2 years ago by
IrK
▴ 100
0
votes
0
replies
12
views
How to select GEO datasets for differential expression analysis using GEO2R
GEO
DEGs
GEO2R
37 minutes ago by
dreamer247
• 0
0
votes
0
replies
25
views
Blog:
Unlocking the Cellular Universe: The Importance of Single-Cell Sequencing in Animal and Plant Research
Single-cell
1 hour ago by
Novogene
▴ 500
0
votes
3
replies
610
views
PopGenome lost individual information
PopGenome
updated 2 hours ago by
kristensen1234
▴ 10 • written 12 months ago by
Yixuan
• 0
1
vote
1
reply
98
views
Question About Handling Technical Replicates in ATAC-seq
technical-replicate
atacseq
updated 7 hours ago by
rfran010
★ 1.4k • written 13 hours ago by
LuciaNhu
▴ 10
12
votes
16
replies
18k
views
8 follow
How to convert vcf to 23andme format
genome
sequencing
SNP
updated 10 hours ago by
ngelbal
• 0 • written 7.5 years ago by
alec_djinn
▴ 390
836
votes
169
replies
172k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
2
replies
117
views
Poor alignment rates using Bowtie
aligment
bowtie2
bowtie
miRNAs
6 hours ago by
omicon
▴ 40
1
vote
2
replies
102
views
Polishing raw nanopore reads with Pacbio
polishing
assembly
updated 4 hours ago by
colindaven
7.4k • written 12 hours ago by
samuel.a.odonnell
▴ 590
0
votes
4
replies
385
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 14 hours ago by
Brian Bushnell
20k • written 6 days ago by
bge
• 0
0
votes
3
replies
181
views
Identifying domain of long-read assembled contig
longread
taxonomy
identification
contig
updated 15 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Gio
• 0
0
votes
1
reply
92
views
Methods for directional pathway analysis of DEGs?
Pathway
ORA
GSEA
analysis
Limma
updated 3 hours ago by
Basti
★ 2.0k • written 17 hours ago by
Steven
• 0
0
votes
3
replies
132
views
Discrepancy between positions on IGV and NCBI's PrimerBLAST
igv
primer
blast
updated 17 hours ago by
GenoMax
150k • written 19 hours ago by
Rozita
▴ 40
0
votes
0
replies
68
views
Why does Radian run so much slower than vanilla R?
R
Python
Radian
VS-Code
19 hours ago by
RR
• 0
4
votes
9
replies
278
views
6 follow
About the Tool FASTP
Quality-control
reads
fastp
updated 11 hours ago by
Ram
45k • written 1 day ago by
AIMAR
• 0
0
votes
0
replies
58
views
Significant SNPs with the same effect in FarmCPU
effect-size
gwas
FarmCPU
likage-disequilibrium
20 hours ago by
AndrMod
• 0
6
votes
11
replies
703
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
21 hours ago by
alexandrakortsi
• 0
0
votes
0
replies
77
views
Job:
Postdoc ML/AI in Genomics & Bioinformatics at Duke University
Postodoc
Genomics
AI
21 hours ago by
alwayshope
▴ 40
0
votes
1
reply
120
views
analyze gene expression of 3 genes in RNA-Seq data
R
RNA-Seq
updated 18 hours ago by
ATpoint
87k • written 22 hours ago by
pinheirofabiano
▴ 100
1
vote
1
reply
350
views
methRead takes too long
MethylKit
updated 23 hours ago by
Alexander Blume
▴ 10 • written 7 months ago by
CTLong
▴ 140
0
votes
0
replies
73
views
rrvgo::getGoSize error
ReViGO
GO-terms
rrvgo
updated 11 hours ago by
Ram
45k • written 1 day ago by
Ana
• 0
0
votes
0
replies
72
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
1 day ago by
Ahmed Jaber
• 0
0
votes
0
replies
89
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
1 day ago by
Bioinformatics_16
• 0
0
votes
1
reply
153
views
Forum:
Questions on what to focus on in the next 3-4 years of my research
Career
offtopic
path
7 hours ago by
Abiodun
• 0
0
votes
7
replies
393
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
11 hours ago by
himanshu0102
• 0
1
vote
2
replies
188
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
2 hours ago by
bioinfo1990
▴ 10
0
votes
0
replies
102
views
News:
Course: Phylogenetic Comparative Methods in R – May 12–16 (Online)
R
Phylogenetic-Comparative-Methods
Ultrametric-Phylogenies
updated 10 hours ago by
Ram
45k • written 2 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
234
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
23 hours ago by
JustinZhang
▴ 120
0
votes
1
reply
503
views
Issues with T2T in pigeon prepare from isoseq
long-read
isoseq
rna-seq
updated 10 hours ago by
Ram
45k • written 6 months ago by
SethJ
• 0
1
vote
1
reply
297
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
updated 3 days ago by
Gordon Smyth
★ 7.9k • written 3 days ago by
Apprentice
▴ 170
1
vote
1
reply
344
views
Missing short indels from vcf
bcftools
shortindels
mpileup
updated 3 days ago by
LauferVA
4.7k • written 6 days ago by
kbranger
• 0
4
votes
6
replies
521
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 3 days ago by
mmhryc
• 0 • written 5 days ago by
harsh
▴ 20
1
vote
2
replies
274
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 3 days ago by
5heikki
11k • written 3 days ago by
Sophia
• 0
4
votes
6
replies
445
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
1 hour ago by
jahnreinhard.ringger
• 0
1
vote
12
replies
573
views
MultiQC_report
adapter
Quality-control
fastqc
multiqc
updated 11 hours ago by
Ram
45k • written 4 days ago by
AIMAR
• 0
4
votes
3
replies
319
views
Forum:
How to get into research for an absolute beginners
research
updated 1 day ago by
Yugan Gogul Muthukumar
▴ 10 • written 4 days ago by
jpeduprep
• 0
0
votes
0
replies
176
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
4 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
263
views
how to do a corellation analysis of multiple CRISPR data sets
crispr-screen
batch-effect
correlation
updated 11 hours ago by
Ram
45k • written 4 days ago by
Assa Yeroslaviz
★ 1.9k
8
votes
4
replies
498
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 3 days ago by
LauferVA
4.7k • written 6 days ago by
shpak.max
▴ 60
1
vote
12
replies
661
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 16 hours ago by
jared.andrews07
★ 18k • written 4 days ago by
Will
• 0
0
votes
0
replies
213
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
protein-design
molecular-modeling
postdoc
updated 11 hours ago by
Ram
45k • written 4 days ago by
Sophie
• 0
1
vote
3
replies
374
views
Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
updated 3 days ago by
1769mkc
★ 1.2k • written 4 days ago by
Alex
• 0
0
votes
1
reply
258
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 4 days ago by
zx8754
12k • written 4 days ago by
ohtang7
▴ 40
1
vote
1
reply
256
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
updated 1 day ago by
ATpoint
87k • written 4 days ago by
karlensberg
• 0
2
votes
9
replies
577
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 4 days ago by
Pierre Lindenbaum
165k • written 5 days ago by
totoroGirl
• 0
1
vote
1
reply
273
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
4 days ago by
Franck
• 0
0
votes
0
replies
196
views
Need help defining a threshold
DAVID
Genes
GO
4 days ago by
Ana
• 0
5
votes
4
replies
377
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 5 days ago by
ATpoint
87k • written 5 days ago by
maplewj
▴ 20
0
votes
1
reply
425
views
Question about `vg construct`
vg
updated 5 days ago by
Jouni Sirén
▴ 630 • written 10 days ago by
zhengluo
• 0
120,919 results • Page
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Recent Votes
Answer: Question About Handling Technical Replicates in ATAC-seq
Comment: Polishing raw nanopore reads with Pacbio
Clarification on sequence duplication levels and Qualimap estimated duplication rate
Comment: About the Tool FASTP
Comment: PCA comparison of cell line vs tumors
Comment: Larger genome size than expected-please help
Answer: Find the reads which correspond to DP of vcf
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Answer: Does EnhancedVolcano() supports crosstalk()?
by
Mauws
• 0
Original Github issues: https://github.com/kevinblighe/EnhancedVolcano/issues/77 https://github.com/kevinblighe/EnhancedVolcano/issues/114…
Comment: Extract length of sample sequence from vcf
by
jahnreinhard.ringger
• 0
unfortunately both of these did not work for my case, as both return the difference between the REF and ALT alleles of all samples, and not…
Answer: PopGenome lost individual information
by
kristensen1234
▴ 10
Hi, I am facing the same problem and was wondering if you found a solution?
Comment: Methods for directional pathway analysis of DEGs?
by
Basti
★ 2.0k
GSEA is directional and will identify gene sets that are regulated in one direction. If you want to use ORA, you could separate up-regulate…
Comment: Polishing raw nanopore reads with Pacbio
by
colindaven
7.4k
I don't know of any tools. The more typical polishing approach would be to assemble the ONT reads first, then polish contigs using more acc…
Comment: Poor alignment rates using Bowtie
by
omicon
▴ 40
Geno, thank you very much for your response. The associated paper doesn’t provide much information… they mention the kit (Ion Total RNA-Se…
Comment: How to identify 16s sequences from binning data(contigs)?
by
Brian Bushnell
20k
Hi Laura, did you solve the problem, or was there something you need in addition to the version on my google drive? I do have a couple oth…
Answer: Question About Handling Technical Replicates in ATAC-seq
by
rfran010
★ 1.4k
> Should I merge these replicates? If yes, should the merging be done at > the FASTQ level, BAM level, or peak level (e.g., overlapping pe…
Comment: Poor alignment rates using Bowtie
by
GenoMax
150k
The data above is likely referenced in this past thread from OP (if it is not please let us know): https://www.biostars.org/p/9609664/ Si…
Comment: How to convert vcf to 23andme format
by
ngelbal
• 0
Can someone please provide me with a tool/sourcecode to convert a VCF into GEDMatch uploadable format?
Comment: Error in importing data from 10x genomics into RStudio
by
himanshu0102
• 0
Yes, that is correct.
Comment: Polishing raw nanopore reads with Pacbio
by
GenoMax
150k
Just a thought. You could make fake illumina reads from HiFi reads.
Comment: Error in importing data from 10x genomics into RStudio
by
1769mkc
★ 1.2k
to help you and at the same time other can help when you can cite what exactly you had ran the code, the Seurat version R session info etc,…
Answer: bbduk.sh trimming to BAM output file
by
Brian Bushnell
20k
Hi Brent, at one time, and to some extent, BBDuk did trimming of sam/bam files. However, it's a very fiddly process because the cigar stri…
Answer: Identifying domain of long-read assembled contig
by
Mensur Dlakic
★ 29k
In my experience, [**tiara**](https://github.com/ibe-uw/tiara) works really well in classifying contigs between the 3 major kingdoms, plus …
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