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0 votes
0 replies
483 views
Finding Indel Mutant structures
indel
written by Logan 0
0 votes
0 replies
808 views
Doublet Detection for Intestinal Immune Cells in scRNA-seq
scdblfinder seurat scrna-seq doublets immune
written by s 0
0 votes
7 replies
4.1K views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated by SanjidaR_NCBI 7 • | written by Bruno Santos 0
0 votes
1 reply
986 views
no "-" strand in transcriptome alignment
drs transcriptome alignment
updated by GenoMax 16K • | written by baibhu1234 6
0 votes
3 replies
2.5K views
What is best way to do CNV Analysis on Xenium data (Spatial transcriptomics)?
seurat xenium spatialtranscriptomics singlecell
updated by yura.grabovska 94 • | written by geno89 2
0 votes
3 replies
1.2K views
Finding a gene in human
variant gene
updated by Ram 4.5K • | written by zizigolu 438
0 votes
4 replies
2.0K views
Assigning cell annotation based on calculated scores.
clustering seurat ucell cell-annotations score
updated by ATpoint 9.1K • | written by Assa Yeroslaviz 197
0 votes
0 replies
544 views
single cell rna seq NMF Error in which.min(sapply(res.runs, "[[", "residuals"))
error sc-rna-seq seurat nmf
updated by Bastien Hervé 680 • | written by Beatriz 0
0 votes
1 reply
907 views
Low quality of NGS SNP analysis panel
fastqc iontorrent ngs
updated by Prash 32 • | written by kate-nelis 0
0 votes
4 replies
1.6K views
Multiple fail points in fastqc file
fastqc report
written by dr.deepakkukkar 0
0 votes
1 reply
953 views
mapping to transcriptome.fasta vs genome.fasta
mapping gtf transcriptome genome
updated by Mensur Dlakic 3.0K • | written by baibhu1234 6
0 votes
2 replies
947 views
Where to find WGS, metagenome data for obesity group?
hmp microbiome data ncbi metagenomics
updated by ehaag 10 • | written by Emily 7
0 votes
2 replies
934 views
WDL 1.0 - Directory Type
directory input wdl
written by davidmaimoun 6
0 votes
1 reply
844 views
How to input INDELs in ped files
snp r haplostats haploview indel
updated by Mwangana 0 • | written by Ant 5
1 vote
0 replies
689 views
Tool: HGVSV: A tool to parse and generate HGVS names with Structural Variant support
variants hgvsv variant hgvs structural
written by parker.payne 1
0 votes
3 replies
1.6K views
P-value calculation between groups in split violin plot
violinplot ggplot singlecellrnaseq
updated by LChart 518 • | written by AB 39
0 votes
3 replies
2.4K views
After doublet detection in 10x scRNA-Seq data, there is still evidence of doublets
r doubletfinder seurat scrna
written by yura.grabovska 94
0 votes
0 replies
608 views
Hash-Based Allele Calling
calling hash allele
written by davidmaimoun 6
0 votes
0 replies
497 views
Issues with FPKM Calculation in RNA-seq Analysis (Apodemus agrarius)
fpkm. cufflinks
updated by lieven.sterck 1.6K • | written by ohtang7 4
1 vote
5 replies
1.6K views
Metagenomics/amplicon sequencing: Most publicly available data already host removed sequences or no?
amplicon decontamination qc microbiome metagenomics
written by Maxwell 7
0 votes
1 reply
979 views
plot PLINK2.0 output with ggtree
ibs matrix plink ggtree
written by Matteo Ungaro 16
0 votes
3 replies
1.0K views
PCA for Batch effect
batch wes pca effect
updated by mark.ziemann 199 • | written by SIMONE 0
0 votes
3 replies
1.1K views
Looking for an old-fashioned alignment editor
msa editor
updated by GenoMax 16K • | written by Suicyte 1
0 votes
0 replies
590 views
eQTL mapping with imputed genotypes: use data from GT or DS slot of VCF?
eqtl vcf imputation matrixeqtl
written by Colari19 10
0 votes
1 reply
763 views
Query on WES
wes
updated by Ram 4.5K • | written by rauf.sania786 0
0 votes
0 replies
674 views
Replace heterozygous genotypes with minor allele in a vcf file
genotype snp vcf heterozygous
written by kumar.vinod81 34
1 vote
4 replies
1.2K views
Enrichment analyses (GO TERM etc)
clusteprofiler somascan proteins enrichment
updated by mark.ziemann 199 • | written by kl 2
0 votes
2 replies
812 views
Protoplast Transient Assay in Arabidposis
transient-assay protoplast arabidposis
updated by dthorbur 350 • | written by Maryam 0
3 votes
2 replies
1.8K views
Plink removing a lot of samples
plink2 plink gwas
written by Steven 5
1 vote
9 replies
2.4K views
How to determine new bacterial species from custom isolate?
species genome submission
updated by michael.ante 408 • | written by marongiu.luigi 79
0 votes
0 replies
475 views
The antibiotic resistome (args_oap, another bioinformatics tools)
resistome metagenome args_oap
updated by Ram 4.5K • | written by aLex97 1
0 votes
0 replies
612 views
News: Gene Set Enrichment Analysis in R/Bioconductor course - Online, March 3-6. Last call
r bioconductor gene-set-enrichment-analysis gsea
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
1 reply
858 views
Read depth for RNA-seq based Variant Calling
mouse read-depth rna-seq variant alignment
updated by Ram 4.5K • | written by vireen105 0
0 votes
4 replies
5.3K views
News: Web Scraping and Text Analysis in R (March 21st - April 11th, 2025) Course
rstats data-analysis web-scraping r
written by Transmitting Science communication 7
1 vote
2 replies
1.4K views
HaplotypeCaller Not Detecting Variants
gatk variant-calling wgs
updated by Ram 4.5K • | written by akshit 1
0 votes
3 replies
1.6K views
NCBI genome submission validation error
genome annotation
updated by lieven.sterck 1.6K • | written by slin023 2
0 votes
1 reply
876 views
Query Regarding Missing Sample Paths in Graph-Based Pangenome Construction
variant-calling pangenome giraffe vg haplotypes
updated by Ram 4.5K • | written by s_135 1
2 votes
4 replies
1.5K views
Variant Missing in VCF but Present in BAM Files: Discrepancy Identified via IGV Report in Join-Call Project
gatk deepvariant bwa
updated by Pierre Lindenbaum 17K • | written by lunping98 2
0 votes
2 replies
894 views
Potential mapping issues in Cas9 knockout cells with STAR (the truncated RNA)
star rna-seq
written by Weize 1
0 votes
3 replies
1.1K views
Normalizing Peaks in ChIP seq
chip-seq
updated by Ram 4.5K • | written by mropri 17
1 vote
0 replies
638 views
Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis
qc microbiome fastp
written by Maxwell 7
0 votes
0 replies
410 views
Estimating the Relative Abundance of a Species in a Mixed Microbial Community Using 16S PCR
16s
written by ljrdain2508 0
0 votes
2 replies
1.4K views
Training Augustus for Gene Prediction
augustus busco genome prediction gene
updated by Buffo 246 • | written by shiv 1
0 votes
1 reply
748 views
Mus musculus genome scaffold discrepancy
genome ncbi
updated by Wayne 208 • | written by SJP 0
0 votes
1 reply
677 views
Edit Dataset FASTQ files using ReadStore Command Line Interface
fastq readstore cli
updated by ATpoint 9.1K • | written by DNAStar 0
0 votes
0 replies
404 views
plyranges – joining gpos object only by the start coordinate of the range
genomicranges plyranges
updated by Pierre Lindenbaum 17K • | written by Kateřina 0
0 votes
1 reply
668 views
Fast querying of variant metrics with database
python database
updated by Pierre Lindenbaum 17K • | written by DBScan 53
1 vote
2 replies
1.0K views
Mitochondrial Variant Calling Tools
mitochondrial ngs variant calling illumina
written by adarsh 8
0 votes
3 replies
7.2K views
How to use harmony with scanpy?
scanpy harmony
updated by Rezin 0 • | written by bioinfo 19
0 votes
2 replies
1.2K views
SpliceAI custom gene annotation file
gencode spliceai
written by ClkElf 5
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