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Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver ATAC-seq Bioinformatics csaw
1 minute ago by Rafael Soler ★ 1.2k
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0
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7
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Job: PhD position for metagenomics analysis at the University of Udine
metagenomics bioinformatics job
11 minutes ago by Fabio Marroni ★ 3.0k
0
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0
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12
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Forum: How does Kraken2 deal with poor read qualities?
kraken qiime2 kraken2 qiime
37 minutes ago by Christopher • 0
0
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0
replies
13
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converting transcript IDs (Ensembl) to gene symbols in R
RNAseq
34 minutes ago by ashkan ▴ 160
0
votes
1
reply
17
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z-score of gene set
z-score scRNA set gene
updated just now by ★ 2.5k • written 49 minutes ago by • 0
3
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5
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358
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Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
55 minutes ago by beantkapoor16 ▴ 10
0
votes
1
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25
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DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN GenomicsDB
updated 30 minutes ago by ▴ 300 • written 1 hour ago by • 0
0
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0
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18
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Last step of metagenome analysis before visualization
metagenome python analyis
1 hour ago by Ayda Ecem • 0
0
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3
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47
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Generating a Bed file from a Fasta file
bedfile Sequences Random NullSeq
updated 1 hour ago by 161k • written 2 hours ago by • 0
0
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3
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1.7k
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Running STRUCTURE from command line
command STRUCTURE unix
updated 2 hours ago by • 0 • written 3.0 years ago by ▴ 10
1
vote
3
replies
511
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Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 3 hours ago by ▴ 160 • written 5 weeks ago by ▴ 40
0
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0
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38
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Calculated LAI is too large
annotation LAI assembly TE genome
5 hours ago by Yao ▴ 30
1
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1
reply
686
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Herald: The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by 2.8k
17
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10
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7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 580
799
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167
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144k
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109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.8k • written 7.5 years ago by 100k
0
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0
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48
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How to recover the entire sequence from all_contig_annotations.csv?
VDJ single-cell TCR-seq cellranger 10x
7 hours ago by dawnyipingzou • 0
0
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2
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85
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Where to find old version of GATK best practice
gatk
updated 1 hour ago by 142k • written 7 hours ago by ★ 1.2k
0
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1
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78
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Nextflow docker: Error response from daemon
sarek gatk4 docker nextflow
updated 7 hours ago by 161k • written 7 hours ago by ▴ 200
0
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0
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48
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News: Online course- Advanced Python for Life Sciences
Python MachineLearning Programming DataVisualisation
8 hours ago by carlopecoraro2 ★ 2.5k
0
votes
1
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80
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CreateSeuratObject taking very long
seurat
updated 2 hours ago by ★ 1.6k • written 11 hours ago by • 0
0
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0
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57
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Multi-ploid data in ANGSD and NGSadmix
ancestry diploid haploid admixture
12 hours ago by Christopher • 0
1
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2
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160
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Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
17 hours ago by ojaswinipandey • 0
0
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2
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126
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Kraken2 Custom Database non-deterministic results
Metagenomics kraken2
58 minutes ago by Bjorn • 0
1
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4
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251
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How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA whole-genome-sequencing NCBI
updated 19 hours ago by 43k • written 21 hours ago by • 0
2
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4
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190
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Filter Genome for Specific Sites
bedtools
updated 19 hours ago by 43k • written 21 hours ago by • 0
0
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3
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209
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Error in using BioSampleParser tool: subscript out of bounds
R
updated 17 hours ago by ▴ 130 • written 1 day ago by ▴ 20
1
vote
1
reply
91
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Generating Group/Cluster Lists from fastq files
Sequencing RNA-seq DNA-Seq
updated 22 hours ago by 142k • written 23 hours ago by • 0
0
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0
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69
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News: Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor Systems-Biology Network-Analysis R
updated 19 hours ago by 43k • written 23 hours ago by ★ 2.5k
2
votes
0
replies
97
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Herald: The Biostar Herald for Monday, May 20, 2024
herald
1 day ago by Biostar 2.8k
2
votes
4
replies
354
views
Super ehancers
enhancers
3 hours ago by Oburah • 0
0
votes
1
reply
100
views
vcf phasing
beagle WhatsHap phasing
updated 2 hours ago by 47k • written 1 day ago by ▴ 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
21 hours ago by sainavyav22 • 0
0
votes
1
reply
589
views
Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 1 day ago by ▴ 40 • written 8 months ago by • 0
1
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2
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161
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 22 hours ago by 43k • written 1 day ago by ▴ 10
0
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3
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171
views
GATK Structural Variants Pipeline - Steps
SV GATK Variant-Calling
updated 23 hours ago by 43k • written 1 day ago by ▴ 20
0
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0
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77
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Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 22 hours ago by 43k • written 1 day ago by ▴ 20
0
votes
1
reply
121
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy GO R
updated 1 day ago by ▴ 130 • written 1 day ago by ▴ 20
0
votes
1
reply
91
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How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by 142k • written 1 day ago by • 0
0
votes
0
replies
70
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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
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 43k • written 1 day ago by ▴ 20
0
votes
0
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89
views
transcriptome annotation
annotation trinity transcriptome
updated 23 hours ago by 43k • written 1 day ago by • 0
0
votes
5
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216
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Why most genes have high padj values
RNA-seq DEG
updated 22 hours ago by 43k • written 1 day ago by • 0
7
votes
14
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2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 1 day ago by ▴ 30 • written 3.1 years ago by • 0
0
votes
1
reply
117
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Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 1 day ago by 82k • written 1 day ago by ▴ 100
0
votes
1
reply
133
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 1 day ago by 11k • written 1 day ago by • 0
0
votes
4
replies
237
views
GO analysis: p-value range
GO R
updated 1 day ago by 4.6k • written 1 day ago by ▴ 20
1
vote
3
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217
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News: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk PlatformPresentation offtopic
updated 6 hours ago by 6.4k • written 1 day ago by • 0
0
votes
3
replies
235
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq seqtk extractionproblem
updated 1 day ago by 142k • written 2 days ago by • 0
0
votes
0
replies
97
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
441
views
Add stats to the plot
R
updated 7 hours ago by ▴ 130 • written 2 days ago by • 0
117,051 results • Page 1 of 2342
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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: z-score of gene set by bk11 ★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
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…
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