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Forum: How is PLINK obtaining p-values and coefficients for linear regression
PLINK GWAS
8 minutes ago by Daiki • 0
3
votes
2
replies
114
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There are a way to align phage reads in to bacterial genomes?
alignment sequences reads
14 hours ago by schlogl ▴ 180
2
votes
4
replies
272
views
No index in the undetermined fastq file
bcl2fastq
updated 17 hours ago by 14k • written 2 days ago by ★ 1.3k
0
votes
0
replies
76
views
News: A Practical Introduction to R with the Tidyverse - Online 2–4 June
Tidyverse R DataAnalysis Quarto ggplot2
1 day ago by Physalia-courses ★ 2.6k
3
votes
0
replies
101
views
TCGA Germline allelic fraction distribution
calling variant tcga
1 day ago by ramiro.barrantes ▴ 50
2
votes
2
replies
203
views
Issue in circular heatmap, the rows value are getting interchanged.
R circos heatmap circularheatmap
updated 1 day ago by 6.3k • written 2 days ago by ▴ 20
837
votes
170
replies
177k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 27 days ago by 3.6k • written 8.5 years ago by 102k
0
votes
2
replies
204
views
STAR alignment not detecting some transcripts / custom reference
star bwa rna-seq alignment scrna-seq
updated 1 day ago by ★ 1.5k • written 1 day ago by • 0
4
votes
5
replies
296
views
How to preserve full FASTQ header through alignment and CRAM recovery
bam fastq cram
updated 1 day ago by 151k • written 1 day ago by ▴ 890
0
votes
3
replies
223
views
error in the output of bedops
human bedtools libraries illumina bedops
updated 1 day ago by 151k • written 2 days ago by ▴ 10
0
votes
3
replies
293
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RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis method rnaseq
updated 1 day ago by ★ 1.5k • written 3 days ago by • 0
0
votes
0
replies
90
views
Job: Bioinformatician - SAGC at SAHMRI Adelaide, South Australia
Bioinformatician
2 days ago by Careers@SAHMRI ▴ 50
53
votes
10
replies
56k
views
11 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 2 days ago by • 0 • written 8.6 years ago by ▴ 590
2
votes
2
replies
474
views
GSEA and Cytoscape Enrichment maps
Cytoscape RNA-seq GSEA
updated 2 days ago by 151k • written 11 days ago by • 0
3
votes
2
replies
276
views
CNVs annotation after CNVkit and clinical databases
Annotation CNVs clinical_database
2 days ago by AIMAR ▴ 10
1
vote
2
replies
218
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant Somatic_data Help Copy
2 days ago by AIMAR ▴ 10
3
votes
0
replies
161
views
Herald: The Biostar Herald for Thursday, May 22, 2025
herald
2 days ago by Biostar 3.6k
0
votes
2
replies
213
views
Correcting Technical Artifacts in Cross-Dataset Pseudobulk Analysis
batcheffect deseq2 pseudobulk
2 days ago by seojin.yang • 0
0
votes
1
reply
497
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE admixture
updated 2 days ago by • 0 • written 18 months ago by • 0
0
votes
3
replies
267
views
Remapping assembled contigs from Flye output file
tools flye remapping bioinformatics aseembly
updated 2 days ago by 151k • written 3 days ago by • 0
2
votes
1
reply
191
views
Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?
pon hg38 vcf mutect2 gatk
updated 3 days ago by 166k • written 3 days ago by • 0
0
votes
0
replies
139
views
Contigs Input For Phylogenetic Tree
contigs phylogeny nextstrain phylogenetics
3 days ago by davidmaimoun ▴ 50
4
votes
3
replies
276
views
assembly tool for plant data
plant
2 days ago by analyst ▴ 60
0
votes
0
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238
views
Will using different Illumina manifest files (with only chr/position changes) affect genotype calling in GSA microarrays?
Illumina manifest microarray GSA
3 days ago by windyday • 0
0
votes
3
replies
285
views
tteximeta problem: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment
teximeta salmon
updated 2 days ago by ▴ 170 • written 3 days ago by ▴ 370
3
votes
3
replies
350
views
Heatmap of rnaseq data with z-score scale
RNA-seq
updated 3 days ago by 14k • written 3 days ago by • 0
0
votes
2
replies
291
views
Z-score for scRNA-seq data?
scRNAseq
3 days ago by S • 0
0
votes
0
replies
166
views
OncodriveFML warnings
cancer_driver selection_analysis driver_genes oncodrivefml
3 days ago by yahn ▴ 10
0
votes
2
replies
374
views
European Variation Archive submission eva-sub-cli validation failure: "Sample name concordance check"
eva-sub-cli EuropeanVariationArchive submission database
updated 4 days ago by • 0 • written 5 days ago by • 0
0
votes
0
replies
217
views
Job: Project Research Scientist-I (Bioinformatics – Next Generation Sequencing Data Analysis) - India
Biology Computational Bioinformatics
updated 3 days ago by 7.5k • written 4 days ago by • 0
0
votes
0
replies
185
views
News: online course: AI for Genomics: from CNNs and LSTMs to TRANSFORMERS
Transformers CNN Genomics LSTMs AI
4 days ago by Physalia-courses ★ 2.6k
0
votes
1
reply
630
views
Anyone familiar with studies on computational neuroscience focused on consciousness, particularly in anatomical areas such as ARAS?
neuroscience computational
updated 4 days ago by 6.3k • written 4 days ago by • 0
0
votes
1
reply
237
views
Evaluating Large CRISPR/Cas9 Deletions (~300 kb) in F0 Xenopus Embryos
CRISPR large mosaic Cas12a F0 deletion
updated 3 days ago by 151k • written 4 days ago by • 0
3
votes
15
replies
751
views
6 follow
Trim CDS to ORF
codon CDS offset transcripts
updated 1 day ago by 7.5k • written 4 days ago by ▴ 30
1
vote
3
replies
307
views
Multi-omic trajectory on CITE-Seq data
multiomic 10x single-cell transcriptomics trajectory
updated 3 days ago by 88k • written 4 days ago by ★ 1.7k
10
votes
22
replies
976
views
STAR aligner problem on local laptop
RNA-sequencing
3 days ago by Morris_Chair ▴ 370
3
votes
8
replies
1.4k
views
Mageck RRA is listing negative controls as high fold change in the gene summary
python crispr mageck
updated 4 days ago by ★ 18k • written 11 months ago by • 0
0
votes
1
reply
238
views
RNA-seq analysis
STAR HiSat2 featurecounts
updated 4 days ago by ★ 1.5k • written 4 days ago by • 0
2
votes
2
replies
273
views
Obtaining Q30/Q60 Values from Fastq Files
phred quality illumina rna-seq
updated 4 days ago by 151k • written 4 days ago by ▴ 50
0
votes
1
reply
497
views
Phylogeny aware alignment input
HoSeq MSA
updated 4 days ago by • 0 • written 11 months ago by • 0
0
votes
5
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425
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 days ago by erikatatianacs • 0
1
vote
2
replies
304
views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated 4 days ago by 151k • written 5 days ago by ▴ 10
3
votes
10
replies
600
views
RNASeq bulk transcriptomics analysis
RNASeq Trimgalore genecounts STAR fastqc
updated 2 days ago by 15k • written 5 days ago by ▴ 70
0
votes
1
reply
242
views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 5 days ago by 151k • written 5 days ago by • 0
0
votes
2
replies
290
views
Download GenomicSEM reference file
GenomicSEM
updated 5 days ago by ★ 1.3k • written 5 days ago by • 0
9
votes
11
replies
615
views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem bwa alignment
updated 2 days ago by 4.7k • written 5 days ago by ▴ 890
0
votes
0
replies
215
views
News: UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization genomics cancer
5 days ago by Mary Goldman • 0
0
votes
0
replies
217
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization deseq2 host-pathogen rna-seq
5 days ago by r-ninja ▴ 20
0
votes
0
replies
217
views
Does vg stats support gaf file?
vg
5 days ago by Wang Cong ▴ 20
1
vote
1
reply
260
views
Longest Protein per Gene from gpff file
Protein gpff
updated 5 days ago by 15k • written 5 days ago by ▴ 300
121,233 results • Page 1 of 2425
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STAR do i need --twopassMode ?
DESeq2 outliers-should I be concerned?
Perturb seq
Unexpected negative correlation between gene-length and counts
Cross-species differential gene expression, finding orthologs
RNASeq bulk transcriptomics analysis
How to preserve full FASTQ header through alignment and CRAM recovery
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Recent Replies
Comment: There are a way to align phage reads in to bacterial genomes? by schlogl ▴ 180
Thanks GenoMax
Comment: There are a way to align phage reads in to bacterial genomes? by GenoMax 151k
> Can I use bwa, star or any alignment prog to try to align some phage reads/dna against bacterial genomes? Aligners are data agnostic so…
Answer: No index in the undetermined fastq file by swbarnes2 14k
Run bcl2fastq or bcl-convert yourself, and the indices might turn up.
Answer: Issue in circular heatmap, the rows value are getting interchanged. by Bastien Hervé 6.3k
Open an issue [here][1] In [circos.heatmap][2] vignette, on the first heatmap, you can guess the row R71 in the block "a". With C10/C9 as …
Comment: How to input INDELs in ped files by Mwangana • 0
@Ant, I have the same issue. Did you successfully resolve it?
Comment: terminal can't activate base automatically (conda) by tllee • 0
I ran into the same problem recently. I tried: conda config --set auto_activate_base true Then I checked the `~/.condarc` file. After…
Comment: How to perform Linkage Disequilibrium (LD) analysis in INDELS by Mwangana • 0
@Ant, you can can convert your data into a VCF file by using VCF-Simplify https://github.com/everestial/VCF-Simplify
Comment: How to perform Linkage Disequilibrium (LD) analysis in INDELS by Mwangana • 0
@dthorbur, I have the same issue. Fortunately my data is in a VCF file. Can you please guide me by outlining the steps how to carryout the …
Comment: RNAseq meta-analysis to identify “consistently expressed” genes by rfran010 ★ 1.5k
Just adding on, the problem really is that you cannot say if a gene is not expressed just because it's not detected. I think your approach …
Comment: Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid by rfran010 ★ 1.5k
Also, an alternative method would be to quantify gene expression independently of haplotypes and just quantify variant percentage of the ge…
Comment: Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid by rfran010 ★ 1.5k
Yes, I don't think it's too common, but it should fit easily into isoform/allele-aware quantification workflows, no?
Comment: STAR alignment not detecting some transcripts / custom reference by rfran010 ★ 1.5k
> To debug the source of the problem, I manually aligned my fastq files > to a fasta file containing just the dcm gene using bwa. This repo…
Comment: STAR alignment not detecting some transcripts / custom reference by GenoMax 151k
What is this gene supposed to do? Is it being integrated in zebrafish genome and then expected to be expressed? Are there other genes in …
Comment: How to preserve full FASTQ header through alignment and CRAM recovery by GenoMax 151k
> I delete FASTQ files after alignment to save space Are you never going to need to submit this data to a resource like SRA? Or do you ha…
Comment: How to preserve full FASTQ header through alignment and CRAM recovery by GenoMax 151k
> This seems hacky though Then you can use `reformat.sh` from BBMap suite with option `underscore=t` to convert white space in read names …
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