This is a test version of Biostars. For the public version, visit https://www.biostars.org.
2 votes
9 replies
2.4K views
Find "phased segments" from trio VCF?
phased vcf genotyping variants phasing
written by cmdcolin 448
0 votes
1 reply
1.1K views
Fatal error while doing MD simulation in gromacs related to residuetypes.dat
error docking gromacs md molecular simulation
updated by Mensur Dlakic 3.0K • | written by Tiara 0
4 votes
5 replies
3.8K views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pydeseq2 rna-seq
updated by Lhl 76 • | written by Julia Ma 15
1 vote
0 replies
650 views
Conventions for designing flowcharts for bioinformatics workflows
workflow flowchart diagram pipeline
updated by Ram 4.5K • | written by kalavattam 85
0 votes
4 replies
1.3K views
Difference in reads per cell between samples
seurat scrnaseq
written by taylor.pio 0
0 votes
4 replies
1.3K views
variant calling and filtering
vcftools samtools bcftools
updated by lieven.sterck 1.6K • | written by Paul 0
0 votes
0 replies
736 views
How best to classify consensus SVs merged from multiple callers
sv annotation variants nanopore wgs
written by eebloom 11
0 votes
2 replies
889 views
Annotation of long non-coding RNAs
long noncoding rna
written by jain72744 1
0 votes
0 replies
864 views
News: Online course: Assembly and Annotation of Genomes - March 17th-21st
genome-annotation nanopore pacbio illumina genome-assembly
written by Physalia-courses 281
2 votes
3 replies
1.1K views
suggestion for alternative splicing event detecting tools under two biological conditions
isoforms transcriptome
written by slin023 2
0 votes
0 replies
898 views
Batch download AlphaFold structures
protein api python structure alphafold
written by Joe 2.2K
0 votes
2 replies
927 views
Help for building Pipeline for Modeller
modeller pipeline
updated by Mensur Dlakic 3.0K • | written by Muhammad Saad 0
0 votes
0 replies
604 views
News: Online Course – Flow Cytometry Data Analysis with R/Bioconductor (March 17-20)
r bioconductor flowcytometry
written by Physalia-courses 281
0 votes
2 replies
983 views
structural variation calling through delly is stuck at Split-read assembly step
short reads assembly
written by Bushra Bibi 8
0 votes
5 replies
1.5K views
Variant calling in tumor/normal pairs is calling heterozygous positions
variant
updated by Shred 163 • | written by ramiro.barrantes 6
0 votes
10 replies
2.3K views
How to create a command that matches 13 characters in each column to be extracted into a new file, and leave behind the unmatched ones
featurecounts
updated by Ram 4.5K • | written by MetagenomicsPlease 0
1 vote
1 reply
1.2K views
Forum: Realistic expectations for the current job market?
career_advice resume job_market resume_advice employment
updated by GenoMax 16K • | written by Mark 1
0 votes
3 replies
1.8K views
Is there a way to download the embeddings of Evo2?
embeddings python evo2
updated by Mensur Dlakic 3.0K • | written by George 3
0 votes
1 reply
771 views
Bacterial genome visualization
plasmid bacteria genome gene
updated by GenoMax 16K • | written by erinda 1
0 votes
12 replies
2.7K views
Manual conversion of VCF genotypes to nucleotide sequence
vcf nucleotide sequence
updated by cmdcolin 448 • | written by endretoth 4
1 vote
1 reply
1.2K views
Current best practice for alignment and quantification for downstream analysis in DESeq2
r deseq2 alignment
updated by Devon Ryan 10K • | written by yura.grabovska 94
0 votes
4 replies
1.8K views
STAR 2.7.11b FATAL ERROR could not open genome file genomeParameters.txt but it is not generated in this version
star
updated by Ram 4.5K • | written by msimmer92 31
0 votes
0 replies
898 views
cytAssist manual alignment failing for visium HD and spaceranger count
spatial-transcriptomics visiumhd space-ranger
updated by GenoMax 16K • | written by npont 3
0 votes
5 replies
1.5K views
Nanopore specific assembly tool of Mitochondria
assembly nanopore mitochondria
updated by colindaven 844 • | written by adarsh 8
1 vote
21 replies
12K views
install Bioconductor package and its dependencies
bioconductor r
updated by karyowgene 0 • | written by alessandrotestori7 42
0 votes
1 reply
807 views
Biostars API Issues
visualization web-scraping api
updated by Ram 4.5K • | written by Samuel Oluwasegun 0
0 votes
0 replies
468 views
interpret ligand_receptor pairs
pairs ligand multinichenetr receptor
written by mayahammoud161 0
0 votes
7 replies
2.8K views
DESeq2: error in checkFullRank(modelMatrix)
deseqdataset design deseq2 rna-seq
updated by Konrad 0 • | written by tilia 0
0 votes
6 replies
1.4K views
Comparability between normalized Counts / TPMs and log2FoldChange
foldchange tpms deseq2 normalized rnaseq counts
written by NorbertK 1
0 votes
1 reply
783 views
Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found
music2
updated by Bastien Hervé 680 • | written by Pumla 0
1 vote
2 replies
1.8K views
Forum: Do you agree with the practice of combing TCGA with GTEx?
gtex tcga
updated by i.sudbery 2.3K • | written by nuorain 4
0 votes
7 replies
3.5K views
Help with Funannotate
genomes funannotate fungus annotation
updated by lieven.sterck 1.6K • | written by SomeOne 33
0 votes
2 replies
804 views
Annotations Tools
annotations for tools
written by abebe1423 0
0 votes
3 replies
1.1K views
Alphafold in colab - homotrimer
homotrimer
updated by dthorbur 350 • | written by sjp24 0
0 votes
0 replies
578 views
Different results with 'clara-parabricks fq2bam' and bowtie2
fq2bam clara-parabricks fastq bowtie2
written by Lars 0
0 votes
0 replies
573 views
GWAS to gene function prediction
annotation vcf gwas prediction gene
written by alnus 0
2 votes
2 replies
1.0K views
miRNAs - Adapters, adapters, adapters i´m so confused
mirna-seq geo adpaters mirnas
updated by Ram 4.5K • | written by omicon 4
0 votes
2 replies
847 views
DEseq2: Advice for model (double interaction ?)
deseq2 matrix dge
written by Picasa 71
0 votes
1 reply
900 views
Kallisto alignment with HPC (SLURM)
slurm hpc kallisto alignment
updated by dsull 781 • | written by tekica 0
0 votes
0 replies
435 views
KEGG pathways
kegg pathways
written by Blue 0
0 votes
4 replies
1.4K views
Protein-Protein Network
cytoscape genes breast-cancer network
updated by Ram 4.5K • | written by abdullah 0
0 votes
5 replies
2.9K views
Correct format for Hi-C matrix before converting to BEDPE
juicer matrix bedpe hi-c
updated by kalavattam 85 • | written by desptsp 0
0 votes
0 replies
648 views
News: Mass Spectrometry and Proteomics using R and Bioconductor course
r bioconductor mass-spectrometry proteomics
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
0 replies
607 views
How to download data from MGRAST
mgrast microbiome metagenome
written by Maxwell 7
0 votes
2 replies
979 views
Gene level expression versus variant-level expression
variant rnaseq
written by ramiro.barrantes 6
0 votes
1 reply
927 views
Java error in BEAST2
beast2 java
updated by Pierre Lindenbaum 17K • | written by Rafae 0
0 votes
10 replies
6.1K views
Bedmethyl file format
bedmethyl methylation
updated by lavigne 0 • | written by njornet 2
0 votes
4 replies
1.6K views
Tool: PIASO, a python toolkit for single-cell data analysis
data-integration scrna-seq normalization scatac-seq spatial-transcriptomics
written by Min 0
2 votes
6 replies
4.9K views
Forum: What is the current state of the beef against UMAP/tSNE in the context of sc trajectory analysis/monocle3?
monocle3 umap single-cell tsne trajectory
written by txema.heredia 31
1 vote
1 reply
1.0K views
Type of Pangenome Type/program to use for fungal isolates of the same species, but have major translocations
visualization pangenome genome alignment
updated by samuel.a.odonnell 86 • | written by Drew 1
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