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46 results • Page
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0
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8
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Forum:
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
11 minutes ago by
Christopher
• 0
0
votes
0
replies
8
views
converting transcript IDs (Ensembl) to gene symbols in R
RNAseq
17 minutes ago by
ashkan
▴ 160
0
votes
0
replies
13
views
z-score of gene set
z-score
scRNA
set
gene
33 minutes ago by
Hien
• 0
3
votes
5
replies
351
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
29 minutes ago by
beantkapoor16
▴ 10
0
votes
1
reply
19
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 10 minutes ago by
DBScan
▴ 300 • written 1 hour ago by
brunomiwa
• 0
0
votes
0
replies
18
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
1 hour ago by
Ayda Ecem
• 0
0
votes
3
replies
43
views
Generating a Bed file from a Fasta file
bedfile
Sequences
Random
NullSeq
updated 1 hour ago by
Pierre Lindenbaum
161k • written 1 hour ago by
pirku
• 0
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
command
STRUCTURE
unix
updated 1 hour ago by
Arthur
• 0 • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
507
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 3 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
38
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
4 hours ago by
Yao
▴ 30
1
vote
1
reply
686
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
47
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
6 hours ago by
dawnyipingzou
• 0
0
votes
2
replies
85
views
Where to find old version of GATK best practice
gatk
updated 1 hour ago by
GenoMax
142k • written 7 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
78
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 7 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
Peter Chung
▴ 200
0
votes
0
replies
47
views
News:
Online course- Advanced Python for Life Sciences
Python
MachineLearning
Programming
DataVisualisation
7 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
73
views
CreateSeuratObject taking very long
seurat
updated 1 hour ago by
Nitin Narwade
★ 1.6k • written 11 hours ago by
eae6d2e7
• 0
0
votes
0
replies
56
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
12 hours ago by
Christopher
• 0
1
vote
2
replies
159
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
17 hours ago by
ojaswinipandey
• 0
0
votes
2
replies
122
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
38 minutes ago by
Bjorn
• 0
1
vote
4
replies
250
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 18 hours ago by
Ram
43k • written 20 hours ago by
Harshita
• 0
2
votes
4
replies
190
views
Filter Genome for Specific Sites
bedtools
updated 18 hours ago by
Ram
43k • written 21 hours ago by
Anita
• 0
0
votes
3
replies
209
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 17 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
1
vote
1
reply
91
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
niruf
• 0
0
votes
0
replies
69
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 18 hours ago by
Ram
43k • written 22 hours ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
97
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
23 hours ago by
Biostar
2.8k
2
votes
4
replies
352
views
Super ehancers
enhancers
2 hours ago by
Oburah
• 0
0
votes
1
reply
98
views
vcf phasing
beagle
WhatsHap
phasing
updated 2 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
2
replies
179
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
20 hours ago by
sainavyav22
• 0
1
vote
2
replies
161
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 21 hours ago by
Ram
43k • written 1 day ago by
Sony
▴ 10
0
votes
3
replies
171
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 23 hours ago by
Ram
43k • written 1 day ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
77
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 21 hours ago by
Ram
43k • written 1 day ago by
ev97
▴ 20
0
votes
0
replies
135
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 18 hours ago by
Ram
43k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
89
views
transcriptome annotation
annotation
trinity
transcriptome
updated 23 hours ago by
Ram
43k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
216
views
Why most genes have high padj values
RNA-seq
DEG
updated 21 hours ago by
Ram
43k • written 1 day ago by
mnx0723
• 0
1
vote
3
replies
217
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 5 hours ago by
colindaven
6.4k • written 1 day ago by
Dr.
• 0
1
vote
8
replies
440
views
Add stats to the plot
R
updated 7 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 18 hours ago by
Ram
43k • written 2 days ago by
Rodolfo Adrián
• 0
0
votes
3
replies
324
views
Trimming tool
Trimming
updated 18 hours ago by
Ram
43k • written 3 days ago by
GeneC
• 0
4
votes
9
replies
622
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 5 hours ago by
marco.barr
▴ 130 • written 5 days ago by
diqixiaoyaoer
▴ 20
1
vote
6
replies
341
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
3 hours ago by
Umer
▴ 50
0
votes
2
replies
266
views
How can I calculate the OS of each patient?
overall-survival
20 hours ago by
Pedro
• 0
0
votes
5
replies
343
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
16 hours ago by
mavy
▴ 10
4
votes
10
replies
844
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 7 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 23 hours ago by
Ram
43k • written 5 months ago by
LauferVA
4.2k
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 4 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
46 results • Page
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Recent Votes
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
A: How To Convert List Of Entrez Ids Into Gene Name
How To Convert List Of Entrez Ids Into Gene Name
A: RSeQC Output from infer_experiment.py - what does it mean?
A: findOverlaps function in R
Comment: What marks a De-Novo Genome assembly as FAILED?
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Recent Replies
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 220
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…
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