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0 votes
2 replies
613 views
Any method to extract k-mer seqs of a specific taxid from KrakenUniq/Kraken database?
krakenuniq kraken
updated by DareDevil DareDevil • written by Depan • Depan
0 votes
4 replies
1.1K views
Multi/Cross Species rnaseq analysis
deseq2 rnaseq salmon
updated by dthorbur dthorbur • written by Tom Brady • Tom Brady
0 votes
1 reply
1.9K views
I performed Homer's annotatePeaks.pl on multiple tissues, yet when I run annotatePeaks on the merged tissues, I get fewer total annotated peaks. Is there an explanation for this?
homer atacseq
updated by Surbhi • Surbhi • written by Ronin • Ronin
0 votes
5 replies
991 views
Pre-processing duplicates in SMARTer-seq data
rna-seq umi fastq smarter-seq fastp
updated by ATpoint ATpoint • written by kiki • kiki
0 votes
1 reply
423 views
Integrating multiple GEO methylation datasets: at which step of preprocessing?
methylation infinium 450k
updated by Arup Ghosh Arup Ghosh • written by Ricardo • Ricardo
0 votes
1 reply
590 views
Truthset NA12878 T2T/Pangenome for benchmarking?
t2t benchmarking pangenome vcf alignment
updated by Arup Ghosh Arup Ghosh • written by smokestack • smokestack
2 votes
0 replies
305 views
Tool: Ligase: Create multi-tool Docker images instantly (no Dockerfile required)
biocontainers software docker reproducibility pipeline
written by matthew • matthew
0 votes
10 replies
1.7K views
Dealing with unclassified metagenomic reads
metagenome
updated by Mensur Dlakic Mensur Dlakic • written by arshad1292 • arshad1292
1 vote
1 reply
493 views
How to quickly make a surjection between Minigraph graph and MC graph in HPRC
vg
updated by colindaven colindaven • written by gulin • gulin
0 votes
5 replies
1.0K views
Whole genome sequencing, different sequencing platforms, different quality control?
wgs snp bacteria
updated by SomeOne • SomeOne • written by yesquokkan • yesquokkan
0 votes
1 reply
1.5K views
SNPduo error reading ped files
ibs genome snpduo ped
updated by muriel.grosb • muriel.grosb • written by amitgourav.ghosh12 amitgourav.ghosh12
0 votes
6 replies
1.5K views
StringTie fails with “Fatal error: Exit code 1” when using GFF3 annotation for a non-model halophyte
stringtie agat rna-seq
updated by Juke34 Juke34 • written by Chamara Lakshitha • Chamara Lakshitha
0 votes
1 reply
492 views
What Tool Are You Using for Transposable Elements Analysis
quantification python transposable-elements
updated by Ram Ram • written by Etornam09 • Etornam09
0 votes
1 reply
510 views
Anyone Using Telescope for Transposable Elements Quantification?
quantification transposable-elements telescope
updated by Ram Ram • written by Etornam09 • Etornam09
0 votes
0 replies
305 views
Is it valid to compare fold enrichment values from separate ORA runs across conditions
ora deg enrichment
written by carolofharvest • carolofharvest
2 votes
12 replies
11K views
filter out fasta File by pattern
fasta awk regexp sed
updated by Ram Ram • written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
0 replies
301 views
News: Advanced Python for Data Science and Bioinformatics course
machinelearning python deeplearning
written by Physalia-courses Physalia-courses
0 votes
1 reply
403 views
Looking for database with per residue conservation score for the whole human proteome
database proteomics dataset conservation
updated by GenoMax GenoMax • written by joko • joko
0 votes
12 replies
1.9K views
How can I find what is wrong with a bulk RNA-seq sample
deg rna-seq
updated by GenoMax GenoMax • written by txema.heredia • txema.heredia
0 votes
0 replies
262 views
Methylation analysis plroblem
volcano value differetial-methylation adjpvalue
updated by Ram Ram • written by Wilo • Wilo
0 votes
3 replies
961 views
Which SPAdes output should be used for genome annotation: contigs.fasta or scaffolds.fasta?
wgs
written by Abhijit • Abhijit
0 votes
1 reply
388 views
miRNA Cluster Related
cluster mirna
updated by GenoMax GenoMax • written by shrinka.genetics • shrinka.genetics
1 vote
5 replies
1.0K views
Would it be possible to run cellranger count after umi_tools extract?
quantification umi_tools single-cell cellranger
written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
0 replies
322 views
News: DNA methylation course - online 20-24 April
nanopore dnamethylation evolution pacbio
written by Physalia-courses Physalia-courses
0 votes
6 replies
4.9K views
seqtk subseq command not pulling full fastq reads
next-gen sequencing
updated by ATpoint ATpoint • written by kalanir • kalanir
0 votes
5 replies
1.4K views
Forum: Opinions on - Is the "AI Bioinformatics Startup" model sustainable, or will internal pipelines win?
career service bioinformatics startups
updated by Istvan Albert Istvan Albert • written by buhbs • buhbs
0 votes
3 replies
1.1K views
I’m looking for input on how to interpret a large structural variant call from Manta, particularly in the context of additional SV signals inside the duplicated region.
ploidy interperation tag
updated by Ram Ram • written by Juvol • Juvol
0 votes
0 replies
347 views
Is there a bioinformatics metric that uses codon degeneracy to predict protein mutational vulnerability?
protein codon
updated by Ram Ram • written by Kis Norbert Levente • Kis Norbert Levente
0 votes
8 replies
1.8K views
TRRUST v2 down , how to get trrust_rawdata.[].tsv
trrust human mouse tf
updated by Arup Ghosh Arup Ghosh • written by Lila M Lila M
1 vote
1 reply
798 views
Job: Senior Bioinformatics Engineer (Antibody Discovery) | MiLaboratories | Bilbao, Spain | 90k - 120k EUR
antibody bioinformatics software-engineering immunology
updated by GenoMax GenoMax • written by Stanislav • Stanislav
0 votes
6 replies
1.1K views
Can beta values fall outside 0-1 range?
microarray
written by biod • biod
0 votes
1 reply
579 views
Best practices for generating realistic simulated metagenomic samples for benchmarking?
benchmarking camisim simulated-samples
updated by Ram Ram • written by anna • anna
1 vote
1 reply
729 views
Which is the current standard, ARS-UCD1.2 or ARS-UCD2.0?
cow reference
updated by GenoMax GenoMax • written by mary.v.volkova • mary.v.volkova
0 votes
0 replies
296 views
News: Workshop: Virtual RNA-seq Analysis, February 24-26, 2026
rnaseq workshop uconn
written by zsc25001 • zsc25001
0 votes
0 replies
263 views
Variant calling RADseq and WGS population genomic datasets
population-genomics variant-calling
updated by Ram Ram • written by Stephen • Stephen
0 votes
2 replies
700 views
GATK FilterMutectCalls
mutect2 somatic-variants gatk filtermutectcalls
updated by Istvan Albert Istvan Albert • written by sk_24 • sk_24
0 votes
3 replies
771 views
Weird RNAseq coverage profile
igv splicing rnaseq
updated by benformatics benformatics • written by coolmattmonkey • coolmattmonkey
0 votes
0 replies
356 views
Can vg giraffe align to a subset of the HRPC pangenome graph (e.g. one chromosome)?
giraffe alignment pangenomics indexing vg
written by Karam • Karam
2 votes
2 replies
802 views
Tool: SeqTUI: A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA).
rust sequence alignment viewer phylogenomics
written by Vincent Ranwez • Vincent Ranwez
0 votes
9 replies
6.2K views
best practice for diploid variant calling
variant-calling haplotype samtools diploid bcftools
written by Matteo Ungaro • Matteo Ungaro
0 votes
2 replies
1.1K views
centromere of cattle
centromere cattle
updated by colindaven colindaven • written by Star:) • Star:)
0 votes
7 replies
1.8K views
Tool: BIOSZEN: R/Shiny app for data analysis and visualization from Excel files
microbiology statistics data-analysis data-visualization growth-curves
written by Benjamín • Benjamín
3 votes
3 replies
765 views
Tool: Blini: Lightweight nucleotide sequence search and dereplication
assembly clustering metagenome
updated by Istvan Albert Istvan Albert • written by Amit Lavon • Amit Lavon
0 votes
1 reply
458 views
Query regarding miRNA Expression Status
expression mirna
updated by GenoMax GenoMax • written by shrinka.genetics • shrinka.genetics
0 votes
1 reply
482 views
Are individual-mouse-based statistical tests possible with CellChat?
communication interaction cellchat cell-cell ligand-receptor interactome
updated by ATpoint ATpoint • written by omer.shomrat • omer.shomrat
1 vote
0 replies
361 views
De-noising OMIM phenotypes for multi-gene CNVs/SVs: what heuristics do you use?
omim genomics
written by sameer • sameer
0 votes
5 replies
2.9K views
Dating Common Ancestor
ngs vcf
updated by Dara • Dara • written by Adrian Pelin Adrian Pelin
1 vote
0 replies
318 views
Tool: Quickly Build Your Own GEOmetadb with geokit
geo geometadb geoquery
written by Yun • Yun
0 votes
2 replies
1.1K views
Best tool to annotate open reading frames (ORFs) in virus metagenomics?
dna virus metagenomics
updated by Ram Ram • written by maria.seg • maria.seg
0 votes
1 reply
704 views
Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequences.2bit' ... Error in .TwoBits_export(mapply(.DNAString_to_twoBit, object, seqnames), ...
bsgenome bsgenomeforge
written by Nguyen • Nguyen
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