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0 votes
4 replies
1.2K views
Unable to filter chromosomal coordinates with bcftools
snpeff vcf bcftools
written by beepboop • beepboop
1 vote
6 replies
2.1K views
Slow BLAST speed when database on external drive?
blast
updated by Darked89 Darked89 • written by theclubstyle • theclubstyle
0 votes
3 replies
1.2K views
Read counts from quantmode of Star and Stringtie
star stringtie
updated by ATpoint ATpoint • written by giacuong171 • giacuong171
0 votes
3 replies
1.9K views
Monocle3 gene expression dot plot with a cell data set object (need help with reordering x-axis)
scrna-seq monocle3 celldataset
updated by Ram Ram • written by seattlescientist_01 • seattlescientist_01
1 vote
4 replies
2.7K views
Docker container with multiple SNP calling tools
docker snp genotyping
updated by Ram Ram • written by anikcropscience • anikcropscience
0 votes
1 reply
837 views
How can one annotate a VCF file and transform it into a list of genes with specified mutations?
trimming annotation vcf
updated by GenoMax GenoMax • written by emilydolivo5 • emilydolivo5
1 vote
8 replies
14K views
GSEA preranking metric for RNA Seq
rna-seq gsea deseq2
updated by V_Vibes • V_Vibes • written by bipin • bipin
0 votes
2 replies
5.8K views
VCFtools calculate SNP density
vcf snp vcftools snp-density
updated by ahusnoo • ahusnoo • written by christinachavez • christinachavez
0 votes
0 replies
789 views
Perform a Nested Permanova in r
permanova vegan r adonis
written by Mgs3 • Mgs3
0 votes
1 reply
752 views
How do I summarise the structure of the oligo library I made
nanopore-sequencing ssdna alignment gtf
written by Mar • Mar
0 votes
0 replies
1.1K views
I met error when running CellChat "cellchat <- computeCommunProbPathway(cellchat)"
cellchat
written by lujingyi • lujingyi
0 votes
2 replies
1.7K views
calculating p-value for GO terms
go_id
updated by GenoMax GenoMax • written by azadeh.taati • azadeh.taati
0 votes
1 reply
837 views
the order genes in the gene list on the topGO
enrichment-analysis topgo go-term p-value
updated by Ram Ram • written by azadeh.taati • azadeh.taati
1 vote
0 replies
639 views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
written by brian.fristensky brian.fristensky
0 votes
3 replies
1.2K views
csaw - is there a way to identify composition bias in a dataset?
chip-seq csaw normalization composition-bias
updated by ATpoint ATpoint • written by GLG • GLG
0 votes
2 replies
955 views
Big differences between biological replicates makes DESeq2 result 0
deseq2 chip-seq
updated by Ram Ram • written by rebw25 • rebw25
0 votes
3 replies
1.4K views
How to find out sample type information of '.rna_seq.augmented_star_gene_counts.tsv' files in TCGA?
star_gene_counts tcga
written by Anamika Acharyya • Anamika Acharyya
0 votes
0 replies
473 views
Comparing relative expression of a conserved gene between distantly related species.
rnaseq comparativegenomics normalization
written by georgii.vdovin • georgii.vdovin
0 votes
2 replies
1.5K views
Should centering and scaling be done on methylation beta values for principal component analysis (PCA)?
pca pcatools
written by Pratik Pratik
0 votes
0 replies
942 views
Troubleshooting error with BSmooth: `error in serialize(data, node$con)`
r sequencing methylation bsseq
updated by Ram Ram • written by Jautis Jautis
0 votes
2 replies
1.6K views
Bowtie2 and Hisat2 read mapping comparisons
hisat2 bowtie2
updated by Ram Ram • written by Allan • Allan
0 votes
5 replies
2.2K views
How to find genomic locations of SNP probes in EPIC chips
microarray snp epic
written by Bosberg • Bosberg
0 votes
1 reply
865 views
Primer design for genomic DNA given mRNA transcripts
mrna gene dna primer-design
updated by Ram Ram • written by Simon • Simon
0 votes
0 replies
628 views
sniffles2 on multiplex amplicon using nanopore technology
sniffles
written by safeassli • safeassli
0 votes
0 replies
636 views
News: EMBL-EBI Training | Systems biology: from large datasets to biological insight
systems
written by EMBL Events EMBL Events
0 votes
1 reply
1.1K views
Multi-species RNA-seq comparsion
rna-seq transcriptomics
updated by Matthias Zepper Matthias Zepper • written by weather • weather
0 votes
1 reply
634 views
Merging sequence files for metagenomics?
ngs metagenomics
updated by GenoMax GenoMax • written by natrix36 • natrix36
0 votes
9 replies
2.3K views
fill-from-fasta doesnt fill missing values in REF
bcftools variant-calling vcf
written by Serij´s • Serij´s
0 votes
4 replies
1.4K views
Blastn - matches with another species
blast blastn
written by davidmaimoun • davidmaimoun
0 votes
0 replies
501 views
Sliding window of the HGT-DB: Database for Horizontally Transferred Genes
horizontally-transferred-genes
updated by Ram Ram • written by laoshuboi • laoshuboi
3 votes
1 reply
968 views
The eternal two-stop shop between Bethesda and Hinxton
databases ncbi ebi
updated by GenoMax GenoMax • written by cdsouthan cdsouthan
0 votes
8 replies
2.7K views
nfcore/fetchngs : Error: fasterq-dump cannot create this file
fasterq-dump sra sratools fetchngs
updated by pbioinf • pbioinf • written by Pierre Lindenbaum Pierre Lindenbaum
0 votes
0 replies
630 views
Normalization of allelic counts for allele-specific expression analysis
allelic-ratio allelic-counts normalization allele-specific-expression rna-seq
updated by Ram Ram • written by ema • ema
0 votes
0 replies
475 views
Error in intraspotCorrelation function (limma package): Max iterations exceeded??
microarray two-color limma intraspotcorrelation
updated by GenoMax GenoMax • written by Erfan • Erfan
0 votes
4 replies
2.6K views
Colocalization Coloc - Error in if (min(p) > warn.minp)
colocalization coloc
updated by Maristella • Maristella • written by J • J
0 votes
5 replies
1.6K views
DNA Methylation count
methylation
written by Mamatha Y S • Mamatha Y S
0 votes
0 replies
1.2K views
Meta analysis using METAL
gwas metal
updated by Ram Ram • written by khn khn
0 votes
2 replies
1.9K views
Question on how to include TAXIDs when running blast on database
ncbi blastn taxid blast makeblastdb
updated by GenoMax GenoMax • written by Mani • Mani
2 votes
16 replies
14K views
fpkm to tpm conversion
r next-gen
updated by DareDevil DareDevil • written by sayamsmruti • sayamsmruti
0 votes
2 replies
915 views
polygenic risk scores calculation
polygenic-risk-score
written by Eliza • Eliza
0 votes
0 replies
430 views
mapping phospho sites
phosphoproteomics
updated by Ram Ram • written by mirshahvaladi • mirshahvaladi
0 votes
3 replies
3.4K views
Disappearing CB, the bam tag after samtools sort -t CB
sequencing samtools rna-seq
updated by liu2005678 • liu2005678 • written by akh22 akh22
0 votes
12 replies
3.6K views
Is it possible to access the code of a bioinformatics article?
publication
updated by Zhenyu Zhang Zhenyu Zhang • written by sil_bioinfo • sil_bioinfo
0 votes
3 replies
1.6K views
How can we be sure that this module preservation is comparing the same module genes in the two groups?
module-preservation wgcna
updated by Ram Ram • written by Gail • Gail
1 vote
1 reply
1.7K views
Problem running DeepTMHMM with Docker
docker deeptmhmm
updated by Alex • Alex • written by Elizabeth • Elizabeth
0 votes
4 replies
1.7K views
Help interpreting Samtools Flagstat results
star samtools rna-seq
updated by swbarnes2 swbarnes2 • written by ablanchette • ablanchette
0 votes
0 replies
720 views
Parsing error when using sstacks
stacks sstacks
updated by Ram Ram • written by Hayler Edu • Hayler Edu
0 votes
3 replies
1.2K views
Annotate wormbase genes
rna-seq
written by leranwangcs • leranwangcs
0 votes
3 replies
1.3K views
Its possible to merge GTF files from different genome versions so I can assing the seqnames from one ot another
genome gtf
updated by Ram Ram • written by Nicolas • Nicolas
0 votes
1 reply
1.4K views
Clustering sequences in a pandas dataframe
pandas python clustering
updated by dthorbur dthorbur • written by ba2so • ba2so
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