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CNVs annotation after CNVkit and clinical databases
Annotation CNVs clinical_database
55 minutes ago by AIMAR ▴ 10
0
votes
2
replies
48
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant Somatic_data Help Copy
2 hours ago by AIMAR ▴ 10
2
votes
0
replies
34
views
Herald: The Biostar Herald for Thursday, May 22, 2025
herald
3 hours ago by Biostar 3.6k
837
votes
170
replies
177k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 24 days ago by 3.6k • written 8.5 years ago by 102k
0
votes
1
reply
40
views
Correcting Technical Artifacts in Cross-Dataset Pseudobulk Analysis
batcheffect deseq2 pseudobulk
updated 3 hours ago by 88k • written 3 hours ago by • 0
0
votes
1
reply
390
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE admixture
updated 3 hours ago by • 0 • written 17 months ago by • 0
0
votes
3
replies
125
views
Remapping assembled contigs from Flye output file
tools flye remapping bioinformatics aseembly
updated 4 hours ago by 151k • written 12 hours ago by • 0
0
votes
1
reply
73
views
Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?
pon hg38 vcf mutect2 gatk
updated 8 hours ago by 166k • written 8 hours ago by • 0
0
votes
0
replies
40
views
Contigs Input For Phylogenetic Tree
contigs phylogeny nextstrain phylogenetics
8 hours ago by davidmaimoun ▴ 50
3
votes
2
replies
99
views
assembly tool for plant data
plant
updated 3 hours ago by ★ 2.1k • written 9 hours ago by ▴ 60
0
votes
1
reply
73
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis method rnaseq
updated 4 hours ago by 88k • written 9 hours ago by • 0
0
votes
0
replies
86
views
Will using different Illumina manifest files (with only chr/position changes) affect genotype calling in GSA microarrays?
Illumina manifest microarray GSA
15 hours ago by windyday • 0
0
votes
2
replies
107
views
tteximeta problem: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment
teximeta salmon
updated 20 minutes ago by 151k • written 19 hours ago by ▴ 370
3
votes
3
replies
204
views
Heatmap of rnaseq data with z-score scale
RNA-seq
updated 23 hours ago by 14k • written 1 day ago by • 0
0
votes
2
replies
156
views
Z-score for scRNA-seq data?
scRNAseq
20 hours ago by S • 0
0
votes
0
replies
75
views
OncodriveFML warnings
cancer_driver selection_analysis driver_genes oncodrivefml
1 day ago by yahn ▴ 10
0
votes
2
replies
250
views
European Variation Archive submission eva-sub-cli validation failure: "Sample name concordance check"
eva-sub-cli EuropeanVariationArchive submission database
updated 1 day ago by • 0 • written 2 days ago by • 0
0
votes
0
replies
119
views
Job: Project Research Scientist-I (Bioinformatics – Next Generation Sequencing Data Analysis) - India
Biology Computational Bioinformatics
updated 1 day ago by 7.5k • written 1 day ago by • 0
0
votes
0
replies
95
views
News: online course: AI for Genomics: from CNNs and LSTMs to TRANSFORMERS
Transformers CNN Genomics LSTMs AI
1 day ago by Physalia-courses ★ 2.6k
0
votes
1
reply
162
views
Anyone familiar with studies on computational neuroscience focused on consciousness, particularly in anatomical areas such as ARAS?
neuroscience computational
updated 1 day ago by 6.3k • written 1 day ago by • 0
0
votes
1
reply
124
views
Evaluating Large CRISPR/Cas9 Deletions (~300 kb) in F0 Xenopus Embryos
CRISPR large mosaic Cas12a F0 deletion
updated 1 day ago by 151k • written 1 day ago by • 0
2
votes
14
replies
538
views
Trim CDS to ORF
codon CDS offset transcripts
21 hours ago by jaredbernard ▴ 30
1
vote
3
replies
192
views
Multi-omic trajectory on CITE-Seq data
multiomic 10x single-cell transcriptomics trajectory
updated 8 hours ago by 88k • written 1 day ago by ★ 1.7k
10
votes
22
replies
749
views
STAR aligner problem on local laptop
RNA-sequencing
1 day ago by Morris_Chair ▴ 370
0
votes
0
replies
137
views
Tool: Grabstract: Turn complex scientific texts and PDFs into graphical abstracts, scientific posters, journal club slide decks, and more!
visualisation
1 day ago by Anand • 0
3
votes
8
replies
1.3k
views
Mageck RRA is listing negative controls as high fold change in the gene summary
python crispr mageck
updated 1 day ago by ★ 18k • written 11 months ago by • 0
0
votes
1
reply
139
views
RNA-seq analysis
STAR HiSat2 featurecounts
updated 1 day ago by ★ 1.5k • written 2 days ago by • 0
1
vote
2
replies
167
views
Obtaining Q30/Q60 Values from Fastq Files
phred quality illumina rna-seq
updated 2 days ago by 151k • written 2 days ago by ▴ 50
0
votes
1
reply
418
views
Phylogeny aware alignment input
HoSeq MSA
updated 2 days ago by • 0 • written 11 months ago by • 0
0
votes
5
replies
272
views
The allele with index 2 is not defined in the REF/ALT columns" error after AF filtering with gnomAD Exome
gnomAD bcftools vcf
2 days ago by erikatatianacs • 0
1
vote
2
replies
195
views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated 1 day ago by 151k • written 2 days ago by ▴ 10
2
votes
10
replies
456
views
RNASeq bulk transcriptomics analysis
RNASeq Trimgalore genecounts STAR fastqc
updated 2 hours ago by 15k • written 2 days ago by ▴ 60
0
votes
1
reply
148
views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 2 days ago by 151k • written 2 days ago by • 0
0
votes
2
replies
194
views
Download GenomicSEM reference file
GenomicSEM
updated 2 days ago by ★ 1.3k • written 2 days ago by • 0
9
votes
10
replies
432
views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem bwa alignment
updated 2 days ago by 88k • written 2 days ago by ▴ 880
0
votes
0
replies
130
views
News: UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization genomics cancer
2 days ago by Mary Goldman • 0
0
votes
0
replies
135
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization deseq2 host-pathogen rna-seq
2 days ago by r-ninja ▴ 20
0
votes
0
replies
133
views
Does vg stats support gaf file?
vg
2 days ago by Wang Cong ▴ 20
1
vote
1
reply
173
views
Longest Protein per Gene from gpff file
Protein gpff
updated 3 days ago by 15k • written 3 days ago by ▴ 300
2
votes
4
replies
679
views
Modify read groups in BAM file
samtools BAM picard DRAGEN
updated 3 days ago by ★ 1.3k • written 6 weeks ago by • 0
2
votes
1
reply
185
views
Integration of NanoString CosMx FOVs
Spatial transcriptomics
updated 3 days ago by 6.3k • written 3 days ago by • 0
1
vote
2
replies
244
views
Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid plant assembly
RNA-seq
8 hours ago by Zephy • 0
0
votes
1
reply
411
views
News: 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop RNA-Seq transcriptomics VariantCalling DNA-Seq
3 days ago by ecSeq Bioinformatics ▴ 20
0
votes
0
replies
163
views
q-value threshold for omics data when performing univariate cox analysis
MachineLearning q-value Cox FDR omics
3 days ago by Yugan Gogul Muthukumar ▴ 10
6
votes
8
replies
492
views
Cross-species differential gene expression, finding orthologs
orthologs xSpecies stringtie Differential-expression
3 days ago by fe94 ▴ 10
0
votes
3
replies
297
views
Unexpected negative correlation between gene-length and counts
rna-seq bias normalisation
updated 1 day ago by ★ 1.5k • written 3 days ago by ▴ 20
0
votes
1
reply
236
views
Perturb seq
perturbseq
updated 4 days ago by 151k • written 4 days ago by • 0
4
votes
4
replies
1.7k
views
Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq NGS pipeline INDELs SNVs
updated 4 days ago by 151k • written 7 days ago by • 0
1
vote
1
reply
293
views
How important are allele fractions when calling variants?
GATK bacteria BCFTools
updated 3 days ago by 23k • written 4 days ago by • 0
0
votes
0
replies
287
views
Job: Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
nucleosomes post_doc cancer_detection generativeAI bioinformatics
3 days ago by Jakob Skou • 0
121,225 results • Page 1 of 2425
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Answer: CNVs annotation after CNVkit and clinical databases
Answer: CNVs annotation after CNVkit and clinical databases
The Biostar Herald for Thursday, May 22, 2025
Answer: Best way to compare two samples in a VCF file
The Biostar Herald for Thursday, May 22, 2025
Answer: assembly tool for plant data
Comment: Multi-omic trajectory on CITE-Seq data
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Recent Replies
Comment: CNVs annotation after CNVkit and clinical databases by AIMAR ▴ 10
Thanks very much for you help.
Comment: tteximeta problem: couldn't find matching transcriptome, returning non-ranged Su by tarek.mohamed ▴ 370
I updated the post with the code for index building
Answer: CNVs annotation after CNVkit and clinical databases by liushuailong001 ▴ 20
AnnotSV: an integrated tool for structural variations annotation https://academic.oup.com/bioinformatics/article/34/20/3572/4970516 h…
Comment: Proposal on CNV (Copies Variants Numer) analysis tools by AIMAR ▴ 10
I've consulted the documentation and reported an issue in the GitHub site but, since there I've no reply. And I've tried to understand and…
Comment: Proposal on CNV (Copies Variants Numer) analysis tools by GenoMax 151k
> but it doesn't provide very clear documentation. Documentation for `CNVkit` appears to be extensive https://cnvkit.readthedocs.io/en/st…
Comment: Correcting Technical Artifacts in Cross-Dataset Pseudobulk Analysis by ATpoint 88k
Does the design even allow batch correction? Like, are replicates of all groups in all datasets? If not then all this %mt inclusion and stu…
Comment: ADMIXTURE Freezes Right Before Completion by pereyra.s • 0
Same happens to me. Did you find a solution?
Comment: PRS result interpretation by Sam ★ 4.8k
I'd suggest you to read on the basics of PRS before you get started. A good starting place would be this: https://www.nature.com/articles/s…
Comment: assembly tool for plant data by Dave Carlson ★ 2.1k
This is exactly right. It will not be a productive use of your time to try to assemble any polyploid plant genome with only short reads.
Comment: RNAseq meta-analysis to identify “consistently expressed” genes by ATpoint 88k
> There seems to be a lack of standardised methods for identifying consistently expressed genes without differential analysis. OR maybe I a…
Comment: Remapping assembled contigs from Flye output file by GenoMax 151k
> how I can remap this assembled contigs against a reference genome as the number of contigs are very high. That may indicate a "not so we…
Comment: Create local Blast database alias with blastdb_aliastool fails by GenoMax 151k
Good you found a solution. This is a particular issue because of the way you are doing things. Consider accepting my original answer (gree…
Answer: Remapping assembled contigs from Flye output file by colindaven 7.5k
You can map contigs vs a related reference genome with a tool like Ragtag https://github.com/malonge/RagTag. This scaffolding makes more se…
Comment: Create local Blast database alias with blastdb_aliastool fails by etienne • 0
**I found the problem!** I manage the DB folder using `.ncbirc` on Linux and `ncbi.ini` on WIndows, so BLASTDB is well defined. In my Wind…
Answer: Remapping assembled contigs from Flye output file by lieven.sterck 15k
Plenty of tools to choose from: MUMmer, Mauve, Lastz, .... just to name a few. Google with the term 'genome to genome alignment' will gi…
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