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121,890 results • Page 17 of 2438
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4
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5
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2.4k
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Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq NGS pipeline INDELs SNVs
updated 3 months ago by 3.4k • written 4 months ago by ▴ 10
1
vote
1
reply
569
views
How important are allele fractions when calling variants?
GATK bacteria BCFTools
3 months ago by andean • 0
0
votes
0
replies
879
views
Job: Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
nucleosomes post_doc cancer_detection generativeAI bioinformatics
4 months ago by Jakob Skou • 0
0
votes
2
replies
2.0k
views
Analysing Problem Seen In MEGA X
Alignment MEGAX Muscle
updated 4 months ago by • 0 • written 3.9 years ago by • 0
0
votes
0
replies
482
views
discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
Analysis Enrichment
written 4 months ago by • 0
4
votes
2
replies
688
views
DESeq2 outliers-should I be concerned?
deseq2
updated 4 months ago by 89k • written 4 months ago by ▴ 160
1
vote
2
replies
714
views
Trimmomatic command
STAR RNASeq Trimmomatic
updated 4 months ago by 15k • written 4 months ago by ▴ 70
1
vote
1
reply
603
views
Blog: Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
updated 4 months ago by ★ 4.3k • written 4 months ago by ▴ 510
4
votes
9
replies
1.7k
views
Facing issue with output of nextflow pipeline
output nextflow fastqc issue
updated 4 months ago by 7.9k • written 5 months ago by ▴ 20
6
votes
2
replies
1.1k
views
Forum: Pie Charts: to use or not to use
pie-chart graphs
updated 4 months ago by 22k • written 4 months ago by • 0
1
vote
1
reply
501
views
Minimum Number of Cells for Downstream Analysis after subsetting a particular cell type (scRNAseq)?
cell single
updated 4 months ago by 89k • written 4 months ago by ▴ 10
0
votes
3
replies
864
views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif NCBI_genome_database Acinetobacter_guillouiae Nitrogenase Nitrogen_fixation
updated 4 months ago by 153k • written 4 months ago by • 0
0
votes
1
reply
500
views
Target prediction
protien prediction Target
updated 4 months ago by ★ 3.1k • written 4 months ago by • 0
6
votes
12
replies
1.7k
views
Heatmap of a transformed deseq object with pheatmap
deseq2 pheatmap
4 months ago by caroline.zanchi • 0
0
votes
0
replies
403
views
CNVkit CNVs call with threshold issues
CNVkit threshold_log2 Somatic_variant
4 months ago by AIMAR ▴ 70
2
votes
6
replies
1.0k
views
PRS result interpretation
risk score PRS interpretation polygenic
3 months ago by trkfs ▴ 10
2
votes
1
reply
540
views
More rare variants than common variants
PLINK GWAS
updated 4 months ago by 5.1k • written 4 months ago by ▴ 20
1
vote
1
reply
604
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated 4 months ago by ▴ 760 • written 4 months ago by • 0
0
votes
0
replies
879
views
Job: Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD learning bioinformatics deep genomics
4 months ago by bjdaigle ▴ 10
5
votes
4
replies
983
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates Omics Pooling
updated 4 months ago by 5.1k • written 4 months ago by • 0
2
votes
1
reply
576
views
Regressing variables for finding Differentially expressed genes
batcheffect seurat bias scRNASeq
updated 4 months ago by 6.5k • written 4 months ago by ▴ 390
0
votes
0
replies
835
views
Job: Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany e14
4 months ago by elsalatino • 0
1
vote
1
reply
634
views
Alternatives to WGCNA
WGCNA
updated 4 months ago by 5.1k • written 4 months ago by ▴ 10
10
votes
9
replies
1.3k
views
RNA-seq analysis
Htseq-count HiSat2 featurecounts STAR
updated 3 months ago by 153k • written 4 months ago by ▴ 10
2
votes
2
replies
1.6k
views
Liquid Biopsy datasets
RNA-Seq next-gen liquid biopsy miRNA cDNA
updated 4 months ago by ▴ 100 • written 5.0 years ago by • 0
1
vote
4
replies
1.5k
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 4 months ago by ▴ 100 • written 14 months ago by • 0
4
votes
3
replies
1.5k
views
Metagenomics mock datasets
metagenomics
updated 4 months ago by ▴ 100 • written 20 months ago by • 0
3
votes
0
replies
543
views
News: NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics NCBI codeathon
4 months ago by MirianT_NCBI ▴ 800
1
vote
1
reply
573
views
Using structure prediction approaches to predict interaction between two proteins
protein prediction structure
updated 4 months ago by ★ 30k • written 4 months ago by ▴ 30
3
votes
3
replies
703
views
How to visualize Combat-seq corrected counts
batch-correction combat-seq
4 months ago by as823jk • 0
3
votes
6
replies
918
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
4 months ago by 1769mkc ★ 1.3k
0
votes
1
reply
613
views
Umbrella pathways in KEGG
KEGG R
updated 4 months ago by 3.4k • written 4 months ago by ▴ 550
0
votes
2
replies
523
views
Peptide protein dynamics
Pepdide
updated 4 months ago by 15k • written 4 months ago by • 0
2
votes
4
replies
746
views
variant calling chromosome-wise from WGS data
wgs
updated 4 months ago by 153k • written 4 months ago by ▴ 70
5
votes
5
replies
775
views
Design matrix with uneven patient representation across stages
RNA-seq design-matrix limma
4 months ago by Lucas • 0
1
vote
2
replies
909
views
Forum: The best LLM or any tool to generate legal regex expression string for specific usage?
regex awk sed commands linux
updated 4 months ago by 153k • written 4 months ago by ▴ 140
3
votes
6
replies
2.9k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 4 months ago by 3.4k • written 18 months ago by ▴ 210
0
votes
1
reply
560
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly Transcriptome projects SRA
updated 4 months ago by 15k • written 4 months ago by ▴ 270
6
votes
10
replies
3.5k
views
Minimap2 error in Flye de novo assembly
Flye Minimap2
4 months ago by Nilo ▴ 20
0
votes
0
replies
507
views
How to find hormone related proteins from a list of gene/proteins
R
updated 4 months ago by 45k • written 4 months ago by ▴ 860
0
votes
0
replies
490
views
mtDNA variants from WGS data
mitogenome WGS
updated 4 months ago by 45k • written 4 months ago by • 0
0
votes
1
reply
512
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF LiftoverVcf Merge
updated 4 months ago by ▴ 630 • written 4 months ago by ▴ 250
0
votes
0
replies
455
views
Writing genepop from genind
R genepop genind graph4lg stacks
4 months ago by eaabbott0 • 0
3
votes
4
replies
2.4k
views
Remove all entries with duplicate names from fastq file?
fastq illumina duplicate
updated 4 months ago by ▴ 70 • written 4.3 years ago by ▴ 10
2
votes
1
reply
476
views
Copy Number Variants with CNVKit
CVNs Somatic_variant Recommendations CNVKit
updated 4 months ago by 153k • written 4 months ago by ▴ 70
0
votes
0
replies
436
views
Basecount calculation after alignment to multi-fasta file
multi-fasta sequence bwa consensus samtool alignment
4 months ago by aj • 0
0
votes
0
replies
380
views
TEtranscripts analysis
TEtranscripts
4 months ago by frarodmar17 • 0
0
votes
0
replies
393
views
CVNkit call commande
CVNs CNVKit Somatic_variant
4 months ago by AIMAR ▴ 70
0
votes
6
replies
837
views
FraserDataSet() error in FRASER
R splicing FRASER RNAseq alternative
4 months ago by n_navy ▴ 10
0
votes
1
reply
522
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq DEGs
updated 4 months ago by ▴ 570 • written 4 months ago by ▴ 40
121,890 results • Page 17 of 2438
Recent Votes
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
Answer: Rna-seq data
Answer: What Are Your Most-Used Public Data Repositories?
Answer: activity of unloaded/unassembled Tn5
Comment: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs
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Recent Replies
Comment: magpurify errors by shevch2009 ▴ 20
Strange but there are no such headers or contig names in my fasta files
Comment: replace gene names in gff file by Juke34 9.3k
Yes the --prefix Option exists. There is no count per chromosome. You can do it by splitting your input and analyse one sequence at a time…
Comment: Variant analysis for mouse WES by GenoMax 153k
You could open a new issue and ask the developers of `maftools` if this was something they can add.
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by GenoMax 153k
Do you have the locations/sequence of the regions you are interested in?
Comment: magpurify errors by shevch2009 ▴ 20
Thank you
Comment: magpurify errors by Mensur Dlakic ★ 30k
To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or miss…
Comment: magpurify errors by shevch2009 ▴ 20
Thanks What about phylo-markers module error, I tried to look for it :) But haven't found anything. And why it's not working for some but …
Answer: magpurify errors by Mensur Dlakic ★ 30k
A general answer is to always Google the error message. Hopefully you do that in the future. This is the outcome of Googling `AttributeErro…
Comment: Splice junctions plots for long-read seq data by LChart 5.1k
IGV can view coverage and splice junction sashimi plots. However the plot in the paper looks like it was made with miso. https://miso.readt…
Comment: Yeast reference-based genome assembly by GenoMax 153k
> The gene originates from yeast, What does this mean? Are you putting a gene from a different genus/species into some other yeast? Can yo…
Comment: Variant analysis for mouse WES by alba • 0
Hi, thanks for the suggestion! I’m aware of Ensembl VEP, and in fact, I already have my VCFs annotated with VEP. The challenge I’m facing i…
Answer: Structural Variant identification on pangenome graphs by colindaven 7.9k
There might be something here for you : https://github.com/colindaven/awesome-pangenomes Otherwise, I know creating a pangenome with `mi…
Comment: replace gene names in gff file by ja569116 • 0
Hi @juke34 Is it possible to specify the prefix/ custom gene name to rename all the genes in the gff3 file with AGAT, so that the differen…
Answer: Yeast reference-based genome assembly by colindaven 7.9k
Nanopore reads are long enough to create a full assembly. Why not first try to create a whole genome assembly with a tool like Flye if you …
Comment: Variant analysis for mouse WES by alba • 0
I saw that but it looks like it only works for trinucleotideMatrix() specifically, I was looking to be able to generate rainfallPlot(), for…
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