This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
6 replies
1.6K 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 949 • | written by Chamara Lakshitha 3
0 votes
1 reply
525 views
What Tool Are You Using for Transposable Elements Analysis
quantification python transposable-elements
updated by Ram 4.5K • | written by Etornam09 0
0 votes
1 reply
591 views
Anyone Using Telescope for Transposable Elements Quantification?
quantification transposable-elements telescope
updated by Ram 4.5K • | written by Etornam09 0
0 votes
0 replies
343 views
Is it valid to compare fold enrichment values from separate ORA runs across conditions
ora deg enrichment
written by carolofharvest 6
2 votes
12 replies
11K views
filter out fasta File by pattern
fasta awk regexp sed
updated by Ram 4.5K • | written by Assa Yeroslaviz 197
0 votes
0 replies
335 views
News: Advanced Python for Data Science and Bioinformatics course
machinelearning python deeplearning
written by Physalia-courses 281
0 votes
1 reply
435 views
Looking for database with per residue conservation score for the whole human proteome
database proteomics dataset conservation
updated by GenoMax 16K • | written by joko 0
0 votes
12 replies
2.0K views
How can I find what is wrong with a bulk RNA-seq sample
deg rna-seq
updated by GenoMax 16K • | written by txema.heredia 31
0 votes
0 replies
302 views
Methylation analysis plroblem
volcano value differetial-methylation adjpvalue
updated by Ram 4.5K • | written by Wilo 0
0 votes
3 replies
1.0K views
Which SPAdes output should be used for genome annotation: contigs.fasta or scaffolds.fasta?
wgs
written by Abhijit 0
0 votes
1 reply
420 views
miRNA Cluster Related
cluster mirna
updated by GenoMax 16K • | written by shrinka.genetics 4
1 vote
5 replies
1.1K views
Would it be possible to run cellranger count after umi_tools extract?
quantification umi_tools single-cell cellranger
written by Assa Yeroslaviz 197
0 votes
0 replies
372 views
News: DNA methylation course - online 20-24 April
nanopore dnamethylation evolution pacbio
written by Physalia-courses 281
0 votes
6 replies
4.9K views
seqtk subseq command not pulling full fastq reads
next-gen sequencing
updated by ATpoint 9.1K • | written by kalanir 1
0 votes
5 replies
1.5K views
Forum: Opinions on - Is the "AI Bioinformatics Startup" model sustainable, or will internal pipelines win?
career service bioinformatics startups
updated by Istvan Albert 10K • | written by buhbs 3
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 4.5K • | written by Juvol 0
0 votes
8 replies
1.9K views
TRRUST v2 down , how to get trrust_rawdata.[].tsv
trrust human mouse tf
updated by Arup Ghosh 402 • | written by Lila M 130
1 vote
1 reply
835 views
Job: Senior Bioinformatics Engineer (Antibody Discovery) | MiLaboratories | Bilbao, Spain | 90k - 120k EUR
antibody bioinformatics software-engineering immunology
updated by GenoMax 16K • | written by Stanislav 1
0 votes
6 replies
1.2K views
Can beta values fall outside 0-1 range?
microarray
written by biod 0
0 votes
1 reply
623 views
Best practices for generating realistic simulated metagenomic samples for benchmarking?
benchmarking camisim simulated-samples
updated by Ram 4.5K • | written by anna 7
1 vote
1 reply
895 views
Which is the current standard, ARS-UCD1.2 or ARS-UCD2.0?
cow reference
updated by GenoMax 16K • | written by mary.v.volkova 3
0 votes
0 replies
340 views
News: Workshop: Virtual RNA-seq Analysis, February 24-26, 2026
rnaseq workshop uconn
written by zsc25001 1
0 votes
0 replies
302 views
Variant calling RADseq and WGS population genomic datasets
population-genomics variant-calling
updated by Ram 4.5K • | written by Stephen 0
0 votes
2 replies
766 views
GATK FilterMutectCalls
mutect2 somatic-variants gatk filtermutectcalls
updated by Istvan Albert 10K • | written by sk_24 0
0 votes
3 replies
821 views
Weird RNAseq coverage profile
igv splicing rnaseq
updated by benformatics 426 • | written by coolmattmonkey 3
0 votes
0 replies
382 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 0
2 votes
2 replies
868 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 11
0 votes
9 replies
6.3K views
best practice for diploid variant calling
variant-calling haplotype samtools diploid bcftools
written by Matteo Ungaro 16
0 votes
2 replies
1.1K views
centromere of cattle
centromere cattle
updated by colindaven 844 • | written by Star:) 5
0 votes
7 replies
1.9K 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 0
3 votes
3 replies
789 views
Tool: Blini: Lightweight nucleotide sequence search and dereplication
assembly clustering metagenome
updated by Istvan Albert 10K • | written by Amit Lavon 3
0 votes
1 reply
496 views
Query regarding miRNA Expression Status
expression mirna
updated by GenoMax 16K • | written by shrinka.genetics 4
0 votes
1 reply
527 views
Are individual-mouse-based statistical tests possible with CellChat?
communication interaction cellchat cell-cell ligand-receptor interactome
updated by ATpoint 9.1K • | written by omer.shomrat 0
1 vote
0 replies
393 views
De-noising OMIM phenotypes for multi-gene CNVs/SVs: what heuristics do you use?
omim genomics
written by sameer 4
0 votes
5 replies
3.0K views
Dating Common Ancestor
ngs vcf
updated by Dara 0 • | written by Adrian Pelin 268
1 vote
0 replies
359 views
Tool: Quickly Build Your Own GEOmetadb with geokit
geo geometadb geoquery
written by Yun 9
0 votes
2 replies
1.1K views
Best tool to annotate open reading frames (ORFs) in virus metagenomics?
dna virus metagenomics
updated by Ram 4.5K • | written by maria.seg 0
0 votes
1 reply
730 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 1
0 votes
1 reply
758 views
wf-trio (EPI2ME Desktop) – aggregate_pileup_gvcf failing with exit status 137 despite high-memory system
wf-trio
updated by Pierre Lindenbaum 17K • | written by Yash Sinha 0
2 votes
11 replies
3.5K views
Ensembl genome browser is not working
genome browser ensembl
updated by Ensembl Outreach 0 • | written by funky_roller 2
0 votes
0 replies
348 views
News: Introduction to Python Programming for Biologists course - online, 9-12 February
python ngs programming
written by Physalia-courses 281
0 votes
3 replies
630 views
low FeatureCounts in PBMC data
featurecounts rnaseq
updated by ATpoint 9.1K • | written by Jacek 2
1 vote
0 replies
405 views
Quality control of shotgun metagenomics data
network microbiome
written by yesquokkan 1
0 votes
1 reply
544 views
MSTRG. gene id in differentially expressed gene list!
deseq2 stringtie mstrg
updated by GenoMax 16K • | written by khanald2114 0
0 votes
3 replies
821 views
Forum: Advice on spatial transcriptomics tool
spatial-transcriptomics
updated by ATpoint 9.1K • | written by biofibxen123 0
0 votes
5 replies
1.3K views
Circos plot for contig–contig links supported by PacBio read alignments
pacbio circos
updated by Ram 4.5K • | written by matvergara19 0
0 votes
7 replies
1.8K views
Python in bioinformatics
python
written by ogunjinmirashidat 0
0 votes
5 replies
1.1K views
Public data sets
datasets r
updated by Ram 4.5K • | written by himanshu0102 1
1 vote
15 replies
4.2K views
Forum: Reuse of publicly available datasets
publication rna-seq sequencing
updated by Bourumir 4 • | written by sanathoi 1
0 votes
0 replies
375 views
News: Machine Learning for Multi-Omics Integration - online, 2-4 February
deeplearning machinelearning multiomics omics
written by Physalia-courses 281
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