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1,000 results • Page 4 of 20
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4
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9
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2.6k
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Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by • 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 6 days ago by 82k • written 7.1 years ago by ▴ 80
5
votes
13
replies
1.1k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 5 days ago by 82k • written 6 days ago by ★ 1.7k
1
vote
1
reply
410
views
Plink merge errors.
cygwin64 bed PLINK
6 days ago by Dinmukhamed • 0
0
votes
0
replies
194
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
193
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by Atul K. • 0
3
votes
4
replies
650
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
3 days ago by rahu • 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by 43k • written 6 days ago by ▴ 10
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 6 days ago by 6.4k • written 15 months ago by ▴ 130
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 5 days ago by 14k • written 6 days ago by ▴ 510
0
votes
2
replies
533
views
How to get the reference panel for UKBB
UKBB GWAS clump
6 days ago by 航太郎 • 0
11
votes
12
replies
939
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 6 days ago by 43k • written 7 days ago by • 0
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
6 days ago by Ashok • 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
6 days ago by Ashok • 0
0
votes
0
replies
211
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 7 days ago by 43k • written 7 days ago by ▴ 10
1
vote
1
reply
368
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
7 days ago by otieno43 ▴ 30
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
6 days ago by _quantum_girl_ ▴ 10
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
3 days ago by Javier • 0
1
vote
4
replies
679
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 7 days ago by 43k • written 3 months ago by • 0
0
votes
0
replies
176
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
7 days ago by enferdeflame • 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 4 days ago by ★ 7.0k • written 7 days ago by ▴ 260
0
votes
0
replies
187
views
News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 7 days ago by 43k • written 7 days ago by ★ 2.5k
3
votes
9
replies
789
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 7 days ago by ★ 2.4k • written 7 days ago by • 0
0
votes
1
reply
266
views
10x VDJ (TCR/BCR) BAM to fastq
TCR VDJ BCR 10x
updated 7 days ago by 141k • written 7 days ago by ★ 1.9k
0
votes
1
reply
265
views
DEseq2
RNA-seq DESeq2
updated 7 days ago by 43k • written 7 days ago by • 0
0
votes
0
replies
172
views
News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 7 days ago by 43k • written 7 days ago by ★ 2.5k
4
votes
2
replies
316
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 7 days ago by 8.5k • written 7 days ago by ▴ 20
1
vote
0
replies
174
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
7 days ago by Novogene ▴ 420
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 7 days ago by 43k • written 19 months ago by • 0
3
votes
3
replies
500
views
Korean human genome reference file
GWAS reference imputation
6 days ago by SeoGyun • 0
0
votes
0
replies
157
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 7 days ago by 43k • written 7 days ago by ▴ 10
0
votes
0
replies
175
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
7 days ago by P. • 0
0
votes
0
replies
166
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
7 days ago by ekirsch • 0
1
vote
1
reply
392
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
6 days ago by renan.igor • 0
2
votes
1
reply
259
views
Pediococcus acidilactici sequence analysis
BLAST Gene-Ontology
updated 7 days ago by 43k • written 7 days ago by ▴ 120
3
votes
1
reply
596
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 7 days ago by ▴ 20 • written 19 months ago by ★ 4.3k
0
votes
0
replies
174
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
7 days ago by synat.keam ▴ 100
0
votes
1
reply
266
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 7 days ago by 141k • written 7 days ago by • 0
5
votes
4
replies
618
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
6 days ago by BioinfGuru ★ 1.7k
1
vote
1
reply
272
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf bam bcf snps
updated 7 days ago by 3.9k • written 7 days ago by ▴ 10
0
votes
4
replies
574
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
6 days ago by Kai Xin • 0
1
vote
1
reply
223
views
Retrieve a % coverage for each transcript
RNA-seq
updated 7 days ago by 43k • written 8 days ago by ▴ 40
0
votes
1
reply
340
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 8 days ago by ▴ 150 • written 13 days ago by ▴ 40
0
votes
2
replies
367
views
How can I solve this error?
metal
7 days ago by 22211020193 • 0
0
votes
0
replies
164
views
Struggling to lift genome builds
PLINK liftover GWAS
updated 7 days ago by 141k • written 8 days ago by • 0
1
vote
2
replies
269
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 7 days ago by 43k • written 8 days ago by • 0
2
votes
3
replies
410
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
7 days ago by valentinatsar • 0
2
votes
3
replies
302
views
Editing Human Reference Genome by adding a CDS
gff agat transcriptome
updated 8 days ago by 54k • written 8 days ago by ▴ 340
2
votes
10
replies
725
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 7 days ago by 141k • written 8 days ago by • 0
1,000 results • Page 4 of 20
Recent Votes
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold by ginellegrenier • 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot by jkim ▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question by bk11 ★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis? by sp • 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data by Kazo • 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work? by Assa Yeroslaviz ★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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