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News: A Practical Introduction to R with the Tidyverse - Online 2–4 June
Tidyverse R DataAnalysis Quarto ggplot2
3 months ago by Physalia-courses ★ 2.6k
3
votes
3
replies
675
views
TCGA Germline allelic fraction distribution
calling variant tcga
3 months ago by ramiro.barrantes ▴ 60
3
votes
4
replies
840
views
Issue in circular heatmap, the rows value are getting interchanged.
R circos heatmap circularheatmap
3 months ago by Yukta ▴ 30
4
votes
5
replies
1.0k
views
How to preserve full FASTQ header through alignment and CRAM recovery
bam fastq cram
updated 3 months ago by 153k • written 3 months ago by ▴ 890
0
votes
3
replies
721
views
error in the output of bedops
human bedtools libraries illumina bedops
updated 3 months ago by 153k • written 3 months ago by ▴ 10
0
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0
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1.0k
views
Job: Bioinformatician - SAGC at SAHMRI Adelaide, South Australia
Bioinformatician
3 months ago by Careers@SAHMRI ▴ 50
57
votes
10
replies
60k
views
11 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 3 months ago by ▴ 20 • written 8.9 years ago by ▴ 590
2
votes
2
replies
988
views
GSEA and Cytoscape Enrichment maps
Cytoscape RNA-seq GSEA
updated 3 months ago by 153k • written 4 months ago by • 0
3
votes
2
replies
683
views
CNVs annotation after CNVkit and clinical databases
Annotation CNVs clinical_database
3 months ago by AIMAR ▴ 70
4
votes
0
replies
18k
views
Herald: The Biostar Herald for Thursday, May 22, 2025
herald
3 months ago by Biostar 3.6k
0
votes
2
replies
617
views
Correcting Technical Artifacts in Cross-Dataset Pseudobulk Analysis
batcheffect deseq2 pseudobulk
3 months ago by seojin.yang • 0
0
votes
1
reply
835
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE admixture
updated 3 months ago by • 0 • written 21 months ago by • 0
0
votes
3
replies
750
views
Remapping assembled contigs from Flye output file
assembly remapping flye
updated 3 months ago by 45k • written 3 months ago by • 0
2
votes
1
reply
800
views
Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?
pon hg38 vcf mutect2 gatk
updated 3 months ago by 166k • written 3 months ago by • 0
0
votes
0
replies
420
views
Contigs Input For Phylogenetic Tree
contigs phylogeny nextstrain phylogenetics
3 months ago by davidmaimoun ▴ 50
4
votes
3
replies
726
views
assembly tool for plant data
plant
3 months ago by analyst ▴ 70
0
votes
0
replies
654
views
Will using different Illumina manifest files (with only chr/position changes) affect genotype calling in GSA microarrays?
Illumina manifest microarray GSA
3 months ago by windyday • 0
0
votes
3
replies
715
views
tteximeta problem: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment
teximeta salmon
updated 3 months ago by ▴ 180 • written 3 months ago by ▴ 370
3
votes
3
replies
879
views
Heatmap of rnaseq data with z-score scale
RNA-seq
updated 3 months ago by 15k • written 3 months ago by • 0
0
votes
2
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729
views
Z-score for scRNA-seq data?
scRNAseq
3 months ago by S • 0
0
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0
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465
views
OncodriveFML warnings
cancer_driver selection_analysis driver_genes oncodrivefml
3 months ago by yahn ▴ 10
0
votes
2
replies
726
views
European Variation Archive submission eva-sub-cli validation failure: "Sample name concordance check"
eva-sub-cli EuropeanVariationArchive submission database
updated 3 months ago by • 0 • written 4 months ago by • 0
0
votes
0
replies
1.1k
views
Job: Project Research Scientist-I (Bioinformatics – Next Generation Sequencing Data Analysis) - India
Biology Computational Bioinformatics
updated 3 months ago by 3.4k • written 3 months ago by • 0
0
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0
replies
559
views
News: AI for Genomics: from CNNs and LSTMs to TRANSFORMERS Course - (Online, 9-11 Sept)
Transformers CNN Genomics LSTMs AI
10 weeks ago by Physalia-courses ★ 2.6k
0
votes
1
reply
1.4k
views
Anyone familiar with studies on computational neuroscience focused on consciousness, particularly in anatomical areas such as ARAS?
neuroscience computational
updated 3 months ago by 6.5k • written 4 months ago by • 0
0
votes
1
reply
561
views
Evaluating Large CRISPR/Cas9 Deletions (~300 kb) in F0 Xenopus Embryos
CRISPR large mosaic Cas12a F0 deletion
updated 3 months ago by 153k • written 4 months ago by • 0
3
votes
15
replies
1.6k
views
6 follow
Trim CDS to ORF
codon CDS offset transcripts
updated 3 months ago by 7.9k • written 4 months ago by ▴ 30
1
vote
3
replies
716
views
Multi-omic trajectory on CITE-Seq data
multiomic 10x single-cell transcriptomics trajectory
updated 3 months ago by 89k • written 4 months ago by ★ 1.7k
10
votes
22
replies
2.3k
views
STAR aligner problem on local laptop
RNA-sequencing
3 months ago by Morris_Chair ▴ 370
3
votes
8
replies
2.0k
views
Mageck RRA is listing negative controls as high fold change in the gene summary
python crispr mageck
updated 4 months ago by ★ 19k • written 15 months ago by • 0
1
vote
1
reply
517
views
RNA-seq analysis
STAR HiSat2 featurecounts
updated 4 months ago by ★ 1.6k • written 4 months ago by ▴ 10
2
votes
2
replies
681
views
Obtaining Q30/Q60 Values from Fastq Files
phred quality illumina rna-seq
updated 4 months ago by 153k • written 4 months ago by ▴ 70
0
votes
1
reply
747
views
Phylogeny aware alignment input
HoSeq MSA
updated 4 months ago by • 0 • written 15 months ago by • 0
0
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5
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899
views
The allele with index 2 is not defined in the REF/ALT columns" error after AF filtering with gnomAD Exome
gnomAD bcftools vcf
4 months ago by erikatatianacs • 0
2
votes
2
replies
625
views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated 4 months ago by 153k • written 4 months ago by ▴ 20
3
votes
11
replies
1.3k
views
RNASeq bulk transcriptomics analysis
RNASeq Trimgalore genecounts STAR fastqc
3 months ago by rajdeepboral00 ▴ 70
0
votes
1
reply
655
views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 4 months ago by 153k • written 4 months ago by • 0
0
votes
2
replies
649
views
Download GenomicSEM reference file
GenomicSEM
updated 4 months ago by ★ 1.3k • written 4 months ago by ▴ 10
9
votes
11
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1.4k
views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem bwa alignment
updated 3 months ago by 4.7k • written 4 months ago by ▴ 890
0
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0
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487
views
News: UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization genomics cancer
4 months ago by Mary Goldman • 0
0
votes
0
replies
498
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization deseq2 host-pathogen rna-seq
4 months ago by r-ninja ▴ 20
0
votes
0
replies
431
views
Does vg stats support gaf file?
vg
4 months ago by Wang Cong ▴ 20
1
vote
1
reply
470
views
Longest Protein per Gene from gpff file
Protein gpff
updated 4 months ago by 15k • written 4 months ago by ▴ 300
2
votes
4
replies
1.3k
views
Modify read groups in BAM file
samtools BAM picard DRAGEN
updated 4 months ago by ★ 1.3k • written 5 months ago by • 0
2
votes
1
reply
517
views
Integration of NanoString CosMx FOVs
Spatial transcriptomics
updated 4 months ago by 6.5k • written 4 months ago by • 0
2
votes
4
replies
887
views
Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid plant assembly
RNA-seq
updated 3 months ago by ★ 1.6k • written 4 months ago by • 0
0
votes
0
replies
379
views
q-value threshold for omics data when performing univariate cox analysis
MachineLearning q-value Cox FDR omics
4 months ago by Yugan Gogul Muthukumar ▴ 10
7
votes
8
replies
1.1k
views
Cross-species differential gene expression, finding orthologs
orthologs xSpecies stringtie Differential-expression
4 months ago by fe94 ▴ 20
1
vote
3
replies
719
views
Unexpected negative correlation between gene-length and counts
rna-seq bias normalisation
updated 4 months ago by ★ 1.6k • written 4 months ago by ▴ 30
2
votes
1
reply
531
views
Perturb seq
perturbseq
updated 4 months ago by 153k • written 4 months ago by ▴ 20
121,890 results • Page 16 of 2438
Recent Votes
Answer: Stringtie de novo VS reference guided (-G)
Answer: Yeast reference-based genome assembly
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
Answer: Rna-seq data
Answer: What Are Your Most-Used Public Data Repositories?
Answer: activity of unloaded/unassembled Tn5
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Recent Replies
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
Comment: magpurify errors by Mensur Dlakic ★ 30k
There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
Comment: magpurify errors by shevch2009 ▴ 20
Strange but there are no such headers or contig names in my fasta files
Comment: replace gene names in gff file by Juke34 9.3k
Yes the --prefix Option exists. There is no count per chromosome. You can do it by splitting your input and analyse one sequence at a time…
Comment: Variant analysis for mouse WES by GenoMax 153k
You could open a new issue and ask the developers of `maftools` if this was something they can add.
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by GenoMax 153k
Do you have the locations/sequence of the regions you are interested in?
Comment: magpurify errors by shevch2009 ▴ 20
Thank you
Comment: magpurify errors by Mensur Dlakic ★ 30k
To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or miss…
Comment: magpurify errors by shevch2009 ▴ 20
Thanks What about phylo-markers module error, I tried to look for it :) But haven't found anything. And why it's not working for some but …
Answer: magpurify errors by Mensur Dlakic ★ 30k
A general answer is to always Google the error message. Hopefully you do that in the future. This is the outcome of Googling `AttributeErro…
Comment: Splice junctions plots for long-read seq data by LChart 5.1k
IGV can view coverage and splice junction sashimi plots. However the plot in the paper looks like it was made with miso. https://miso.readt…
Comment: Yeast reference-based genome assembly by GenoMax 153k
> The gene originates from yeast, What does this mean? Are you putting a gene from a different genus/species into some other yeast? Are yo…
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