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0 votes
3 replies
218 views
Salmon mapping rate ~50-60% despite 93% STAR unique mapping (decoy-aware index, rRNA-depleted total RNA)
rna-seq transcriptomics salmon alternative splicing
updated by rfran010 174 • | written by mahsa80.mm 0
5 votes
2 replies
180 views
Tool: Benchmarked nf-core/rnaseq across AWS HealthOmics, AWS Batch (on-demand + spot), and our own Nextflow executor — methodology and numbers
nextflow
updated by GenoMax 16K • | written by Derek 5
0 votes
0 replies
161 views
Forum: Looking for a PhD or staff Researcher Position
bioinformatics cancerresearch systemsbiology computationalbiology
updated by Arup Ghosh 402 • | written by Burak Özyürek 1
0 votes
1 reply
120 views
Tool: Protein Structure Annotation Tool
protein annotation structure bioinformatics pymol
updated by GenoMax 16K • | written by Tara 0
0 votes
0 replies
75 views
Having compound name mapping failure in MetaboAnalyst 6.0 ORA/Pathway Analysis
metabolomics metaboanalyst
written by Alvea 0
3 votes
11 replies
36K views
Convert gene name to uniprot ID
gene snp uniprot
updated by Dr. Hend 0 • | written by diablo82.26 3
0 votes
2 replies
158 views
Sorting out doublets in flow cytometry without height or width variables
flowcytometry offtopic
updated by Arup Ghosh 402 • | written by UrbanHuaraches 0
0 votes
13 replies
612 views
Forum: When are you usually on ResearchGate?
work research daytime
written by David Langenberger 1.1K
0 votes
6 replies
351 views
"Memory Used" output for various assemblers is greater than total memory that physically exists on compute node
memory cgroup slurm linux megahit
written by GallopingAvocado 3
0 votes
4 replies
248 views
QC needed previous to DropletQC
dropletqc
written by ae35f6e9 0
0 votes
0 replies
59 views
News: Metagenomic Data Analysis of Microbial Communities (MGMC01) – Live Online Course
metagenomics
updated by GenoMax 16K • | written by coursesinfo 0
0 votes
0 replies
24 views
News: Metagenomic Data Analysis of Microbial Communities (MGMC01) – Live Online Course
metagenomics
updated by Ram 4.5K • | written by coursesinfo 0
0 votes
5 replies
314 views
How can I speed up Deepvariant ?
deepvariant variant caller
updated by Pierre Lindenbaum 17K • | written by DJBill 2
2 votes
10 replies
570 views
Forum: How to start in bioinformatics and system biology in 40 years with PhD in chemistry and IT experience?
bioinformatics biology system
updated by kalavattam 85 • | written by Nikita 3
0 votes
2 replies
167 views
Illumina sequencing data trimming help
illumina trimmomatic fastqc
written by Elena 0
0 votes
3 replies
209 views
Wgcna for a paired study design with only 6 pairs of participants
wgcna
updated by ATpoint 9.1K • | written by Hai Nam 0
0 votes
7 replies
397 views
heterozygosity filter through bcftools
heterozygosity bcftools
written by Bushra Bibi 8
0 votes
1 reply
142 views
Lifting over with rtracklayer vs UCSC
hg38 rtracklayer ucsc hg19 liftover
updated by SeqBench 41 • | written by _quantum_girl_ 8
1 vote
1 reply
296 views
How "bases mapped (cigar)" value in samtools stats is calculated?
samtools
updated by SeqBench 41 • | written by Tian 6
0 votes
11 replies
529 views
Tool: BioNexus: an open-source scientific reliability layer for bioinformatics workflows
scrna software spatial offtopic
updated by Michael Dondrup 5.6K • | written by Herry 0
0 votes
3 replies
419 views
Hisat2 disable spliced alignment or not for DNA shotgun reads??
hisat2 spliced
updated by SeqBench 41 • | written by Jon 3
0 votes
1 reply
346 views
background choice in HOMER motif enrichment
motif homer
updated by SeqBench 41 • | written by sarahmanderni 13
1 vote
1 reply
476 views
What percentage of intronic reads should I expect in single-cell vs single-nuclei?
intronic velocyto single-nuclei
updated by SeqBench 41 • | written by txema.heredia 31
0 votes
1 reply
340 views
Identifying sequence motifs associated with base editing efficiency and mis-editing
base-editing
updated by SeqBench 41 • | written by QX 9
0 votes
1 reply
110 views
Real-time pathogen / microbial detection from raw nanopore signals (no basecalling) ?
edge-computing pathogen-detection raw-signal-analysis nanopore-sequencing genomics
updated by SeqBench 41 • | written by klenehan123 0
0 votes
1 reply
93 views
Illegal instruction error when running GSNAP
gsnap gmap dump core
updated by SeqBench 41 • | written by artemisdiscovery 1
0 votes
1 reply
124 views
Custom background for enrichment analysis with a very small background
olink proteomics enrichment-analysis pathway-analysis
updated by ATpoint 9.1K • | written by Phenylananin 0
0 votes
0 replies
73 views
News: Hands-on NGS Data Analysis Workshops for Researchers
epigenomics rnaseq dnaseq workshops nextflow
written by ecSeq Bioinformatics 9
0 votes
0 replies
60 views
REML analysis through WOMBAT
wombat reml
written by Bushra Bibi 8
0 votes
5 replies
291 views
How to run MrBayes with google VMs?
mrbayes vms google
written by Jeremiah 1
0 votes
0 replies
70 views
News: Online Course: Causal AI Methods for Computational Biology | 2–6 November
multiomics causalinference computationalbiology machinelearning causalai
written by Physalia-courses 281
0 votes
12 replies
600 views
Grouping chromosomes to give them similar labels
genome assemblies fungal hifi
written by SomeOne 33
0 votes
3 replies
197 views
HaploView 4.2: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
haplotype blocks java haploview
updated by cmdcolin 448 • | written by nikos 0
1 vote
3 replies
218 views
NCBI SQN: table2asn doesn't include my transcriptID correctly
sqn annotation ncbi genome
updated by SeqBench 41 • | written by Heleen 1
0 votes
7 replies
382 views
Trimming overhangs from contigs
denovoassembly
updated by lieven.sterck 1.6K • | written by isag 0
0 votes
3 replies
312 views
raw matrices or filtered matrices
cellranger snrnaseq
updated by SeqBench 41 • | written by Zee 0
0 votes
3 replies
242 views
How to integrate multiomic data and predict the disease type?
machine-learning
updated by SeqBench 41 • | written by Ifthekar Hussain 1
0 votes
2 replies
192 views
RNAseq comparison across samples
rnaseq differential rnasequencing expression r
updated by SeqBench 41 • | written by jen.stankev 0
0 votes
1 reply
151 views
Theoretical Idea: Modeling a surface-display cellulase system in human gut bacteria
synthetic-biology
updated by SeqBench 41 • | written by DoGoodGetGood09 0
0 votes
3 replies
237 views
Evigene and ORF prediction
start orf codon evigene
updated by SeqBench 41 • | written by Lucija 0
0 votes
3 replies
241 views
Question about Blast
blast
updated by SeqBench 41 • | written by testbotrr 0
0 votes
4 replies
290 views
Interpretation of Copy number variation graphs generated by NGS
cnv graphs
updated by colindaven 844 • | written by drshahzadbhatti 0
0 votes
0 replies
68 views
News: Workshop: Virtual RNA-seq Analysis, Aug. 25-27, 2026
rnaseq uconn workshop
updated by GenoMax 16K • | written by zsc25001 1
0 votes
1 reply
419 views
Is there a bioinformatics metric that uses codon degeneracy to predict protein mutational vulnerability?
protein codon
updated by SeqBench 41 • | written by Kis Norbert Levente 0
0 votes
5 replies
397 views
Forum: Seeking advice: Preparing for a Bioinformatics MSc abroad & thoughts on paid mentorship communities (e.g., Dean's List)
bioinformatics msc
updated by jared.andrews07 1.9K • | written by Hoangg 0
0 votes
4 replies
293 views
Tool: Looking for feedback on a multi Agent Flow using Langraph, LLM and RAG to identify drug for disease
rag gene langraph llm drugdiscovery
updated by GenoMax 16K • | written by chinmay.cite 0
0 votes
1 reply
113 views
Combining technical repeat with original for a clogged multiome sample?
multiome single cell
updated by SeqBench 41 • | written by Artixiis 0
0 votes
1 reply
639 views
DecontX for ambient RNA removal on 43 samples
snrnaseq rna ambient
updated by SeqBench 41 • | written by kato.nauwelaers 0
0 votes
1 reply
172 views
PySCENIC - Confusion about discrepant results
gene_regulatory_network scenic scrna
updated by SeqBench 41 • | written by jdru 1
1 vote
1 reply
113 views
is someone using the "Strictly Standardized Mean Difference" (SSMD) analysis method?
ssmd
updated by SeqBench 41 • | written by Francois Piumi 8
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