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Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics genetic-variation epistasis snp gnomad
51 minutes ago by SonicSoal • 0
0
votes
0
replies
33
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Rare variants association analysis (using WGS)
variant GWAS rare WGS
4 hours ago by SeoG • 0
0
votes
0
replies
64
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data Breast-Cancer TCGA
updated 5 hours ago by 45k • written 15 hours ago by • 0
0
votes
0
replies
65
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates Omics Pooling
15 hours ago by sardius • 0
0
votes
0
replies
67
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat segmentation anndata visiumhd
updated 16 hours ago by 151k • written 16 hours ago by • 0
837
votes
170
replies
176k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 12 days ago by 3.5k • written 8.4 years ago by 102k
7
votes
7
replies
374
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow workflow pipeline
just now by neng ▴ 30
0
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0
replies
73
views
News: Online course -Reproducibility in Bioinformatics - July 7–9
Singularity Git Docker Snakemake Nextflow
20 hours ago by Physalia-courses ★ 2.6k
1
vote
5
replies
287
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RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA rna-sequencing
22 hours ago by h • 0
0
votes
3
replies
176
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 19 hours ago by 151k • written 23 hours ago by • 0
1
vote
2
replies
179
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Pathway enrichment analysis on time-series data by filtering out age comparisons
pea go rnaseq time-series
16 hours ago by fullycratered • 0
4
votes
4
replies
214
views
building snpeff database for plant
plant
16 hours ago by analyst ▴ 60
1
vote
1
reply
119
views
How to find motif in specific region
motif chip-seq
updated 1 day ago by 36k • written 1 day ago by • 0
0
votes
0
replies
107
views
How to interpret perplexing qcovhsp result in blastx
blastx qcovhsp blastn
15 hours ago by samuel.himes • 0
0
votes
0
replies
90
views
Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF bcftools
1 day ago by Mwangana • 0
0
votes
0
replies
97
views
Best Practices for Integrating RNA-seq Time Series from Multiple Studies with Varying Protocols
differential-expression meta-analysis integration RNA-seq time-series
1 day ago by enee ▴ 20
10
votes
9
replies
4.8k
views
bcftools query add header
bcftools
updated 1 day ago by 151k • written 3.1 years ago by ▴ 750
0
votes
2
replies
224
views
Alternative to PASApipeline
transcriptomics annotation
updated 1 day ago by 7.4k • written 2 days ago by ▴ 160
0
votes
0
replies
108
views
How to Get a Genetic Map, Given the Physical Position and Genotype Data of Markers
genetic-map
updated 1 day ago by 45k • written 1 day ago by • 0
1
vote
7
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2.4k
views
vcftools --weir-fst-pop returns -nan
fst vcftools
updated 2 days ago by 55k • written 2.4 years ago by • 0
0
votes
1
reply
158
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HISAT2 with Cleaned Data
HISAT2 RNASeq
updated 1 day ago by 7.4k • written 2 days ago by • 0
1
vote
1
reply
174
views
Definitions for "differential expression" and "differential abundance" in RNA-seq?
rna-seq deseq abundance differential-expression
updated 1 day ago by 45k • written 2 days ago by • 0
0
votes
5
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310
views
Efficiently find regions in bed file that are within start and end regions of another bed file.
intersect bedtools
updated 1 day ago by 36k • written 2 days ago by • 0
2
votes
4
replies
242
views
16S Libraries With Non-Purified Short Fragments
Sequencing 16S Libraries Magnetic Beads
1 day ago by alenew.am ▴ 10
0
votes
1
reply
185
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How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq cell polyA single
updated 2 days ago by 151k • written 2 days ago by ▴ 10
7
votes
6
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4.9k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2 ChIP-Seq ChromHMM MACS2 CHROMHMM
updated 2 days ago by ▴ 10 • written 5.9 years ago by ▴ 120
4
votes
5
replies
426
views
Editing and Adding to a GTF file
Annotation Gene-ID GTF
updated 1 day ago by 45k • written 4 days ago by ▴ 10
4
votes
2
replies
194
views
Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM bam averag
updated 2 days ago by 88k • written 2 days ago by ▴ 10
3
votes
3
replies
408
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome fastqc shotgun deduplication
updated 2 days ago by 7.4k • written 7 days ago by • 0
0
votes
3
replies
226
views
differential exon usage from Salmon outputs
edgeR diffSpliceDGE DEU salmon
updated 6 hours ago by ★ 7.5k • written 2 days ago by • 0
0
votes
0
replies
130
views
News: online course: Introduction to Genome Annotation
Gene-Prediction Genome-Annotation Gene-Models
2 days ago by Physalia-courses ★ 2.6k
0
votes
2
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873
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct metawrap module
2 days ago by shevch2009 • 0
2
votes
7
replies
397
views
Circular heatmap using circos.heatmap in R
R circos heatmap circularheatmap
updated 1 day ago by 151k • written 3 days ago by • 0
0
votes
0
replies
158
views
Zebrafish phenotype ontology enrichment analyses
ontology zebrafish
3 days ago by Li • 0
0
votes
2
replies
243
views
Sequence Duplication for Single-End 3RAD Data
duplication reduced-representation
2 days ago by Sarah • 0
0
votes
0
replies
159
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg cytoscape
3 days ago by Adrian • 0
1
vote
6
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1.1k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 3 days ago by 45k • written 10 months ago by ▴ 10
0
votes
0
replies
161
views
News: Ancient Metagenomics course - online, May 27-29
ancient-metagenomics aDNA aMeta
3 days ago by Physalia-courses ★ 2.6k
0
votes
1
reply
204
views
Issues running scAPAtrap
scAPAtrap polyA scRNAseq
updated 3 days ago by 151k • written 3 days ago by ▴ 10
5
votes
3
replies
317
views
What are BED files?
BED
updated 3 days ago by 36k • written 4 days ago by • 0
3
votes
8
replies
489
views
ggplot make boxplots more wide
ggplot2 r
4 days ago by Nona ▴ 90
2
votes
1
reply
260
views
Minimum number of samples for multi-omics data integration
multi-omics
updated 3 days ago by 45k • written 4 days ago by ▴ 10
1
vote
0
replies
200
views
News: Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation workshop UConn
4 days ago by zsc25001 ▴ 10
1
vote
1
reply
244
views
Assigning a string variable on Visual Studio using python
python visual-studio
updated 3 days ago by 45k • written 4 days ago by • 0
4
votes
4
replies
380
views
Tool: Gene Exons Painter
Genomics Visualisation Exons Transcripts Isoforms
updated 3 days ago by 4.1k • written 4 days ago by ▴ 70
0
votes
0
replies
198
views
News: Course online:Functional programming in R, May 27-30
R programming functional
4 days ago by soledad.esteban • 0
3
votes
1
reply
283
views
Herald: The Biostar Herald for Monday, May 05, 2025
herald
updated 4 days ago by ★ 4.2k • written 4 days ago by 3.5k
0
votes
0
replies
179
views
How to generate .AED files from .CEL files using Linux (Affymetrix CytoScan HT-CMA 96F)
HT-CMA-96 analysis data affymetrix microarray
4 days ago by genetixs ▴ 20
0
votes
0
replies
192
views
News: Online course - Introduction to GWAS
R GWAS Statistics
4 days ago by Physalia-courses ★ 2.6k
4
votes
3
replies
322
views
Sample level genotype mapping in plink vcf output
VCF
updated 4 days ago by 166k • written 5 days ago by ★ 1.3k
121,142 results • Page 1 of 2423
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Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
Answer: How to find motif in specific region
Mappability file for hg38
C: Mappability file for hg38
Comment: building snpeff database for plant
Comment: building snpeff database for plant
Comment: building snpeff database for plant
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Recent Replies
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing by neng ▴ 30
Yeah, it's a good solution I've tried. The only problem is that the SplitFasta() process has to be finished before it starts. I don't know …
Comment: differential exon usage from Salmon outputs by dsull ★ 7.5k
Providing each exon as an individual transcript will throw off pseudoalignment-type algorithms which assume that each read originated from …
Comment: Create local Blast database alias with blastdb_aliastool fails by GenoMax 151k
Can you set the following variable and see if that helps. BLASTDB=f:/BlastDB/nr/nr export BLASTDB
Comment: building snpeff database for plant by analyst ▴ 60
Is it safe to add -noCheckCds -noCheckProtein in the command or will it skip important information in the resultant database: java -Xm…
Comment: Create local Blast database alias with blastdb_aliastool fails by etienne • 0
Thank you. It is working now with: blastdbcmd -db f:/BlastDB/nr/nr -taxids 1988 -out f:/BlastDB/extract/acti3.fa But it displays thi…
Comment: Pathway enrichment analysis on time-series data by filtering out age comparisons by fullycratered • 0
Ah that makes sense, I hadn't done the DE analysis myself in this case. I will look at doing that, thank you!
Comment: building snpeff database for plant by lieven.sterck 15k
I had a quick look and though it is feasible to change files (and specifically feature names) such that the files correspond to each other …
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing by neng ▴ 30
what I expected: [part_001, /path/to/split/part_001.fasta] [part_002, /path/to/split/part_002.fasta] ... actually data stream…
Comment: STAR aligner - how is quality and correctness tested across builds/releases? by GenoMax 151k
> Coming from a software engineering background Curious as to how many people were part of your team in (I assume) commercial software dev…
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing by Pierre Lindenbaum 166k
I don't understand how your splitfasta works, the output should collect the files under "split". It should be something like: ``` process …
Comment: STAR aligner - how is quality and correctness tested across builds/releases? by Arthur • 0
Fair question - I single out STAR as I believe it's a widely used tool, but I am curious across the board of these 'widely used bioinformat…
Comment: RNA-Sequencing Analysis when control samples paired-end and tumour samples singl by h • 0
Thanks for both your help I will do that!
Comment: STAR aligner - how is quality and correctness tested across builds/releases? by dsull ★ 7.5k
Just curious: why do you want this documentation and why are you singling out STAR? Can you find this documentation for other bioinformatic…
Comment: building snpeff database for plant by analyst ▴ 60
1. sequences.fa (genomic.fna.gz file) 2. genes.gff.gz (genomic.gff.gz file) 3. genes.gtf.gz (genomic.gtf.gz file) 4. protein.fa.gz (protei…
Comment: SPAdes assembler k-mer > default 127 possible? by owen.donohoe • 0
Thanks, these comments are very useful. We ran into installation and memory problems with this process (spades v3.15.2), but we eventually …
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