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1 vote
7 replies
1.5K views
How to deal with intermediate files
procedures data operations
updated by GenoMax GenoMax • written by ramiro.barrantes • ramiro.barrantes
0 votes
1 reply
668 views
Quality control metrics in mmCIF
pdb protein mmcif
updated by dthorbur dthorbur • written by Adrian • Adrian
0 votes
3 replies
1.0K views
phage sequence no alignment to genome
prophage bwa phage genome alignment
updated by GenoMax GenoMax • written by Luwell • Luwell
0 votes
1 reply
921 views
Mitochondrial Annotation Tool
illumina bovine mitochondria
updated by patrickdm • patrickdm • written by adarsh • adarsh
0 votes
1 reply
691 views
Assessing the difference between a de novo assembly and a reference genome
hifiasm mummmer dnadiff
updated by patrickdm • patrickdm • written by andrea • andrea
0 votes
1 reply
1.2K views
HISAT2 or STAR
alignment hisat2 star
updated by rfran010 • rfran010 • written by SpliceAndScript • SpliceAndScript
0 votes
2 replies
919 views
What to do after fastp?
rna-seq fastp alignment
updated by dthorbur dthorbur • written by SpliceAndScript • SpliceAndScript
0 votes
1 reply
940 views
SNP calling from multiple genomes: No valid SNPs
samtools bcftools snp plink wgs
updated by colindaven colindaven • written by emil.paulitz • emil.paulitz
0 votes
0 replies
904 views
ATAC-seq analysis
atac-seq hmmratac calling peak macs3
updated by GenoMax GenoMax • written by sk_24 • sk_24
0 votes
1 reply
736 views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
r bioconductor scrnaseq rnaseq
updated by GenoMax GenoMax • written by bn • bn
0 votes
1 reply
809 views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated by Jordan M Eizenga • Jordan M Eizenga • written by Floren • Floren
0 votes
2 replies
1.6K views
HOMER findMotifsGenome.pl failed compilation
findmotifsgenome.pl motifanalysis homer
updated by 于 • 于 • written by India • India
0 votes
0 replies
767 views
News: Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
statisticalpower gwas imputation
written by Physalia-courses Physalia-courses
0 votes
4 replies
2.7K views
normalize between 2 different platform
rna-seq
updated by linqy • linqy • written by Edalat • Edalat
1 vote
0 replies
506 views
How to normalize bulk TCR-seq data generated by different methods and platforms
tcr
updated by Ram Ram • written by linqy • linqy
0 votes
1 reply
796 views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated by GenoMax GenoMax • written by michael.dhar • michael.dhar
0 votes
4 replies
2.2K views
Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in terms of using repetitive elements to filter peaks
sequence scatac cell single 10xatac
written by gynecoloji • gynecoloji
0 votes
2 replies
989 views
Using VEP custom input
gnomad constraint loeuf vep pli
written by Sd • Sd
0 votes
0 replies
634 views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta stringtie transcriptome bacterial hisat2
written by a58c4637 • a58c4637
1 vote
5 replies
3.0K views
nanopore unaligned bam files
nanopore
updated by colindaven colindaven • written by sarahmanderni sarahmanderni
0 votes
0 replies
658 views
I woudl ike to understnad how to set the aucMaxRank value for my data set
aucell aucmaxrank
written by gogeni5529 • gogeni5529
0 votes
1 reply
746 views
Issue with Package installation in R.
r gcc
updated by GenoMax GenoMax • written by harsh • harsh
3 votes
4 replies
1.9K views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased nebula haplotype wgs gatk
updated by colindaven colindaven • written by biostars • biostars
0 votes
1 reply
742 views
IGV view for Chromatin accessibility ATAC-seq
atac-seq
updated by ATpoint ATpoint • written by Vxike • Vxike
2 votes
2 replies
2.8K views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell scatac-seq signac transcriptomics
updated by Jan • Jan • written by patelk26 patelk26
1 vote
2 replies
1.1K views
WGCNA blockwiseModules function for small datasets
wgcna blockwisemodules
written by ATS • ATS
0 votes
4 replies
1.1K views
How to add GFP in STAR reference?
star
updated by GenoMax GenoMax • written by bioinfo • bioinfo
0 votes
0 replies
861 views
News: Population Genomics Using Ancient DNA Data course
demographicmodels populationgenomics adna genomics
written by Physalia-courses Physalia-courses
0 votes
1 reply
684 views
Can you compare GETx and TCGA miRNA non normalized counts a
comapre to how
updated by ATpoint ATpoint • written by radwa_noreen • radwa_noreen
0 votes
3 replies
1.1K views
ATAC-seq analysis
atac-seq samtools sorting
updated by ATpoint ATpoint • written by sk_24 • sk_24
0 votes
1 reply
553 views
Learn tNGS
tngs
updated by GenoMax GenoMax • written by hang • hang
0 votes
3 replies
1.4K views
Server Requirements for long read data analysis
longreadserver longreadanalysis serverrequirements server
updated by colindaven colindaven • written by genomics_student • genomics_student
0 votes
1 reply
1.4K views
The molecular signatures database (MSigDB) in R
msigdb
updated by marco.barr • marco.barr • written by Kelly • Kelly
2 votes
3 replies
1.4K views
plotProfile Errors of DiffBind
diffbind
written by lijiangres • lijiangres
0 votes
0 replies
1.5K views
Job: Lab Head positions at the WEHI, Melbourne Australia
labhead australia jobposting
written by Gordon Smyth Gordon Smyth
0 votes
0 replies
646 views
Merging single ATAC seq data sets from multiple sample
10x
written by 1769mkc 1769mkc
0 votes
3 replies
1.2K views
GSEA analysis in R
r ranked_list gsea
updated by ATpoint ATpoint • written by rajdeepboral00 • rajdeepboral00
0 votes
8 replies
1.9K views
Use taxdb tp get scientific names in local BLAST output
taxdb sscinames taxonomy makeblastdb blast
updated by GenoMax GenoMax • written by Luca Arbore • Luca Arbore
0 votes
7 replies
4.3K views
Search all SRA data for sequence? Raw reads only
sra ncbi raw reads fastq
updated by Wayne Wayne • written by poppersrules • poppersrules
0 votes
2 replies
1.7K views
Forum: Is this Rosalind inspired project actually useful?
python code-review
written by Andrew • Andrew
0 votes
1 reply
679 views
Subset a GAM (graph alignment) file
pangenome vg vgteam
updated by GenoMax GenoMax • written by Pau • Pau
0 votes
0 replies
690 views
News: Reproducibility in Bioinformatics course
conda singularity docker snakemake nextflow
written by Physalia-courses Physalia-courses
1 vote
0 replies
808 views
Any tips for optimizing an all vs all alignment with minimap2
mapping nanopore genomics minimap2
written by Mark • Mark
0 votes
0 replies
622 views
Mismatch in orthology results from local alignment and phylogenetic analysis.
alignment local phylogeny global
updated by GenoMax GenoMax • written by Shakunthala Natarajan • Shakunthala Natarajan
0 votes
2 replies
953 views
How to automate blasting contigs?
assembly contig blast wgs
written by marongiu.luigi marongiu.luigi
0 votes
0 replies
593 views
Are there tools to find differences in biochemical pathways between organisms?
biochemistry pathways differential
updated by Ram Ram • written by marongiu.luigi marongiu.luigi
0 votes
0 replies
603 views
DiffBind plot.profile error
diffbind biocparallel
written by this_is_me_trying • this_is_me_trying
0 votes
3 replies
1.8K views
News: 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- FINAL CALL --
workshop rna-seq transcriptomics variantcalling dna-seq
written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
3 replies
1.9K views
Random seed in scanpy
scanpy scrnaseq single-cell
updated by ATpoint ATpoint • written by bioinfo • bioinfo
0 votes
1 reply
994 views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
updated by agis.maulana12 • agis.maulana12 • written by Wenhai • Wenhai
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