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1 vote
1 reply
2.6K views
VCF files and Bed tools
vcf bedtools
updated by vickybhai4206 0 • | written by Rna-Seq 5
0 votes
1 reply
189 views
What are the best alternatives to ROC-AUC for validating transcriptomic/gene expression signatures?
roc auc
updated by SeqBench 41 • | written by Pumla 0
0 votes
1 reply
149 views
AI / ML sequence based mRNA half life prediction
halflife mrna ai ml
updated by SeqBench 41 • | written by petergrahamclark 0
0 votes
1 reply
148 views
How to subset features (genes, peaks, cells) scientifically when analyzing single cell multiomics dataset (scRNA-seq + scATAC-seq)?
multi-omics single-cell r
updated by SeqBench 41 • | written by KABILAN 13
0 votes
1 reply
184 views
Handling paired before/after microbiome data
samples paired
updated by SeqBench 41 • | written by benkosta 0
0 votes
1 reply
135 views
MAGeCK MLE design matrix
mageck-mle pooled-screen mageck crispr-screen design-matrix
updated by SeqBench 41 • | written by Matthew 0
0 votes
1 reply
164 views
WGCNA time course study
longitudinal wgcna
updated by SeqBench 41 • | written by Amit 0
0 votes
1 reply
136 views
Unexpected read structure in Ribo-seq libraries prepared with the QIAseq miRNA kit: missing 5′ adapter, 12 variable bases, and very short GC-rich inserts
riboseq
updated by SeqBench 41 • | written by GiovannaPrezia 0
1 vote
1 reply
162 views
What is the correct experimental unit: plot or plant in a randomized complete block design?
experimental design
updated by SeqBench 41 • | written by Dunia Aurora 1
0 votes
1 reply
145 views
Is vg giraffe appropriate for RADseq sequencing reads?
vg radseq
updated by GenoMax 16K • | written by RianeZ 0
0 votes
1 reply
145 views
Extract gene signature from bulk rnaseq and apply to scrnaseq dataset
gene_signature bulk scrnaseq rnaseq
updated by SeqBench 41 • | written by asmariyaz23 1
0 votes
2 replies
335 views
Tool: AI in Biology - ad for VigyanLLM
bioinformatic ai tools
updated by Aditya 0 • | written by Hemant 0
0 votes
1 reply
167 views
What are best practices for which sites to report Ti/Tv on for human WGS QC?
transition transversion
updated by SeqBench 41 • | written by curious 90
0 votes
2 replies
218 views
Forum: Roadmap advice for a biochemistry/biotech grad transitioning into computational cancer biology
metabolomics career-advice cancer-genomics
updated by SeqBench 41 • | written by ndybdaltyf6 0
0 votes
6 replies
504 views
Alternative annotation tools for GO/KEGG enrichment
go kegg wgcna
written by CaERu _no_ korokoro 0
0 votes
0 replies
124 views
Job: Postdoctoral Position at the NIEHS, NC, USA
computational-biology bioinformatics systems-biology
updated by colindaven 844 • | written by anb28636 0
1 vote
1 reply
166 views
Question about constructing a consensus peak file for diffTF
atacseq difftf diffbind
updated by SeqBench 41 • | written by lilithslily 1
2 votes
5 replies
384 views
fold enrichment between genomic regions/loci
statistical-test fold-enrichment variant-calling
updated by SeqBench 41 • | written by Matteo Ungaro 16
0 votes
1 reply
133 views
Merging of vcf data of two different variant callers and two sequencing platforms
variant_calling
updated by SeqBench 41 • | written by buttaasif110 0
0 votes
1 reply
146 views
Predicting functional impact of a rare heterozygous missense variant (p.I294T) in AJAP1: Partial vs. complete LoF?
variant-effects protein-structure
updated by Mensur Dlakic 3.0K • | written by maximilian.info 0
0 votes
3 replies
293 views
DESeq2 results show the opposite log2FoldChange direction compared to the published RNA-seq study
deseq2
updated by Istvan Albert 10K • | written by ashraffouad1998 0
0 votes
1 reply
199 views
How to actually identify which transcription factors are actively regulating a pathway/gene panel
algorithms transcription factor scoring
updated by kalavattam 85 • | written by Parth 0
0 votes
4 replies
283 views
Linkage prune VCF before ML phylogeny inference (e.g. IQ-TREE)?
iq-tree ld snp phylogeny wgs
written by maxrwjones 7
1 vote
3 replies
278 views
Resources for understanding variant calling pipeline outputs
variant calling ngs
updated by Prash 32 • | written by ptalebic 1
0 votes
0 replies
106 views
News: Population Genomics workshop - online, 21–25 September
populationgenomics adna ancientdna
written by Physalia-courses 281
0 votes
1 reply
142 views
Why were no loci realigned after bcftools normalize?
data genetic bcftools snpfiltering normalize
updated by Pierre Lindenbaum 17K • | written by erika.a.dunn 0
0 votes
5 replies
398 views
Issue with FASTQs of 10X Flex with Antibody Capture
scrna 10x
updated by ATpoint 9.1K • | written by 10x_user 0
0 votes
0 replies
88 views
CIBERSORTx Fractions/HiRes: which mixture/signature-matrix combination is actually used internally with S-mode batch correction?
batch-effect deconvolution single-cell-rnaseq microarray cibersortx
updated by Chrs 0 • | written by Francesco 0
0 votes
5 replies
388 views
calculate the median k-mer coverage from a genomic BAM file command- linux
bam k-mer nipt
written by Ajay Narayan 0
0 votes
2 replies
292 views
Detecting real vs artifact inversions in IGV
igv
updated by SeqBench 41 • | written by ahoerl 0
1 vote
1 reply
215 views
Relevance of strand direction in promoter motif analysis.
motif moods promoter transcription
updated by SeqBench 41 • | written by Shakunthala Natarajan 2
0 votes
1 reply
183 views
filter out low quality variants
variant illumina calling filteration
updated by Aditya 0 • | written by a.br.ravichandran 0
0 votes
5 replies
414 views
STAR number of input reads | 0
star rnaseq
written by paxton 0
0 votes
2 replies
299 views
Species matching IgG controls in CUT&RUN experiment
species cut and run igg
updated by Alisa 0 • | written by kevin.stachelek 8
0 votes
1 reply
162 views
How to retrieve STRING preferredName from amino acid sequence using the STRING API?
python api preferredname string-db protein-sequence
updated by SeqBench 41 • | written by anadomingues 0
0 votes
3 replies
275 views
Get average quality score per position in an aligned bam file
nanopore samtools bam phred33 quality
updated by GenoMax 16K • | written by cedric.blais 2
0 votes
1 reply
149 views
Proper Execution of Codon Usage Bias
dnasp mega codon usage
updated by SeqBench 41 • | written by RCMC 1
0 votes
2 replies
189 views
How can I locate the IIS6 region and the L1014F mutation in the full VGSC sequence?
primer design
updated by SeqBench 41 • | written by tahreem 0
0 votes
3 replies
329 views
Tool: Loom - brings fragmented spatial transcriptomics workflows into one platform - need feedbacks
spatial automatic analysis integration transcriptomics
written by Olivia 1
10 votes
8 replies
887 views
Forum: AI for bioinformatics pipeline development. Is it a good idea?
bioinformatics ngs pipelinedevelopment artificialintelligence
updated by zabiullama 3 • | written by David Langenberger 1.1K
0 votes
0 replies
112 views
News: AI-assisted coding directly inside your R session
llms ai r agenticai
written by Physalia-courses 281
0 votes
2 replies
382 views
Forum: Interested to work
student
updated by Arup Ghosh 402 • | written by kvruchitha02 0
0 votes
6 replies
2.6K views
How long should the AAA... sequence be at the end of read, so that fastqc and multiqc consider it as poly- tail
multiqc fastqc polya
updated by GenoMax 16K • | written by poecile.pal 5
1 vote
4 replies
360 views
Tool: Improved prediction of microbial optimal growth temperatures
machine_learning sequence-based_predictions neural_network protein_language_models
updated by GenoMax 16K • | written by Mensur Dlakic 3.0K
0 votes
2 replies
6.3K views
Merging FASTA files
fasta sequences
updated by pinheirofabiano 14 • | written by l.souza 8
0 votes
0 replies
106 views
News: Genomic Prediction of Complex Traits | Live Online Course | Statistical Genomics & Genomic Prediction
complex traits prediction genomic gwas
updated by GenoMax 16K • | written by coursesinfo 0
0 votes
2 replies
260 views
Forum: Experienced bioinformatician, zero UK interviews, what am I missing?
uk jobs bioinformatics
written by adarsh 8
0 votes
5 replies
393 views
Getting the mRNA data from the GEO accession number
geo number mrna accession
updated by Arup Ghosh 402 • | written by rajdeepboral00 7
0 votes
0 replies
88 views
RUVg workflow with DESeq2: covariates in first-pass design, and collinearity between W factors and known covariates
rnaseq deseq2 ruvseq
written by gallimaria657 0
0 votes
1 reply
162 views
Tool: My Project: RNA-seq Differential Expression Report Generator
genomics bioinformatics rnaseq transcriptomics
updated by ATpoint 9.1K • | written by Penpichaya 0
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