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117,043 results • Page
1 of 2341
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Votes
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1
vote
3
replies
489
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Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 1 hour ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
28
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
2 hours ago by
Yao
▴ 30
1
vote
1
reply
680
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
17
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 580
0
votes
0
replies
38
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
4 hours ago by
dawnyipingzou
• 0
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
1
reply
64
views
Where to find old version of GATK best practice
gatk
updated 5 hours ago by
Pierre Lindenbaum
161k • written 5 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
68
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 5 hours ago by
Pierre Lindenbaum
161k • written 5 hours ago by
Peter Chung
▴ 200
0
votes
0
replies
40
views
News:
Online course- Advanced Python for Life Sciences
Python
MachineLearning
Programming
DataVisualisation
5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
49
views
CreateSeuratObject taking very long
seurat
9 hours ago by
eae6d2e7
• 0
0
votes
0
replies
53
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
10 hours ago by
Christopher
• 0
1
vote
2
replies
153
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
15 hours ago by
ojaswinipandey
• 0
0
votes
1
reply
112
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 16 hours ago by
GenoMax
142k • written 17 hours ago by
Bjorn
• 0
1
vote
4
replies
245
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 16 hours ago by
Ram
43k • written 18 hours ago by
Harshita
• 0
2
votes
4
replies
188
views
Filter Genome for Specific Sites
bedtools
updated 16 hours ago by
Ram
43k • written 18 hours ago by
Anita
• 0
0
votes
3
replies
205
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 15 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
1
vote
1
reply
88
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 20 hours ago by
GenoMax
142k • written 20 hours ago by
niruf
• 0
0
votes
0
replies
66
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 16 hours ago by
Ram
43k • written 20 hours ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
93
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
21 hours ago by
Biostar
2.8k
2
votes
4
replies
336
views
Super ehancers
enhancers
1 hour ago by
Oburah
• 0
0
votes
1
reply
83
views
vcf phasing
beagle
WhatsHap
phasing
updated 20 minutes ago by
WouterDeCoster
47k • written 21 hours ago by
safeassli
▴ 10
0
votes
2
replies
177
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
18 hours ago by
sainavyav22
• 0
0
votes
1
reply
586
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 22 hours ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
158
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 19 hours ago by
Ram
43k • written 1 day ago by
Sony
▴ 10
0
votes
3
replies
169
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 21 hours ago by
Ram
43k • written 1 day ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
73
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 19 hours ago by
Ram
43k • written 1 day ago by
ev97
▴ 20
0
votes
1
reply
117
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 23 hours ago by
marco.barr
▴ 130 • written 1 day ago by
sooni
▴ 20
0
votes
1
reply
89
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
0
replies
68
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
128
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 16 hours ago by
Ram
43k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
87
views
transcriptome annotation
annotation
trinity
transcriptome
updated 21 hours ago by
Ram
43k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
212
views
Why most genes have high padj values
RNA-seq
DEG
updated 19 hours ago by
Ram
43k • written 1 day ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 1 day ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
115
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
130
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 1 day ago by
Ali
• 0
0
votes
4
replies
234
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
1
vote
3
replies
208
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 3 hours ago by
colindaven
6.4k • written 1 day ago by
Dr.
• 0
0
votes
3
replies
231
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 1 day ago by
GenoMax
142k • written 2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
94
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
8
replies
431
views
Add stats to the plot
R
updated 5 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
4
replies
321
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
1
vote
2
replies
349
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 1 day ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
108
views
handling bio replicates for chromHMM
replicates
chromHMM
1 day ago by
Hasan_Daaboul
• 0
0
votes
0
replies
100
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 day ago by
DGTool
▴ 20
0
votes
1
reply
162
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
rj.rezwan
• 0
0
votes
2
replies
313
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
1 day ago by
Ezequiel
• 0
2
votes
0
replies
185
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
2 days ago by
micah
▴ 30
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 16 hours ago by
Ram
43k • written 2 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 2 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
723
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 2 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
117,043 results • Page
1 of 2341
Recent Votes
Comment: What marks a De-Novo Genome assembly as FAILED?
A: How to extract specific chromosome from vcf file
A: How To Filter Mapped Reads With Samtools
C: Filtering A Sam File For Quality Scores
A: Filtering A Sam File For Quality Scores
Comment: Super ehancers
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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Recent Replies
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 210
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
Answer: Pruning Phylogenetic Trees and Bootstrap Values
by
Klaus S
▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
Comment: What is the amount of sequencing data produced annually?
by
Mohamed
• 0
Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 130
what a pity...
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Yes, I can. But there are only two factors that affect my data PCA distribution: groups and donor. And the rest is regarded as residual. …
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
colindaven
6.4k
Please delete this as it has nothing to do with the topic of this forum, bioinformatics. Thanks
Comment: Add stats to the plot
by
marco.barr
▴ 130
if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
Comment: Nextflow docker: Error response from daemon
by
Pierre Lindenbaum
161k
you should ask : https://github.com/nf-core/sarek/issues/
Comment: Where to find old version of GATK best practice
by
Pierre Lindenbaum
161k
https://github.com/gatk-workflows ?
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
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