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Help for Pooled Exome Sequencing SNP Analysis
GATK SNP Exome polymorphisms
4 minutes ago by alejandro.mejiam1 ▴ 20
0
votes
0
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14
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KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization DEG KEGG R pathway
10 minutes ago by txema.heredia ▴ 240
0
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0
replies
16
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MACS3 Parameter adjustments
human libraries illumina callpeak macs3
51 minutes ago by María José ▴ 10
3
votes
2
replies
220
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DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
updated 4 hours ago by 88k • written 23 hours ago by • 0
0
votes
1
reply
60
views
Interactive UMAP scanpy
UMAP scanpy interactive
updated 4 hours ago by 3.4k • written 5 hours ago by ▴ 10
5
votes
5
replies
119
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Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
Batchcorrection VOOM DEGanalysis Limma bulkRNA
updated 4 hours ago by 88k • written 6 hours ago by ▴ 10
5
votes
6
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348
views
Log2FC track Visualization in IGV
visualization IGV RNASeq
2 days ago by SomeOne ▴ 220
840
votes
170
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180k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 8 weeks ago by 3.6k • written 8.6 years ago by 102k
0
votes
0
replies
37
views
News: online course: Sex Chromosome Evolution - 6–10 October 2025
SexChromosome Evolution Genomics
6 hours ago by Physalia-courses ★ 2.6k
0
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0
replies
47
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GSEA of sugarcane
GSEA
8 hours ago by analyst ▴ 70
3
votes
4
replies
387
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DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic Feeding DESeq2 RNAseq
16 hours ago by Cristina • 0
1
vote
12
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372
views
FeatureCount : Successfully assigned alignments is low
rnaseq featurecount
6 hours ago by HarperReed • 0
1
vote
2
replies
138
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN calling IgG peak
5 hours ago by Basti ★ 2.1k
7
votes
3
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273
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custom BED to UCSC genome browser
browser ucsc ucsc-genome-browser genome methylation bed
1 day ago by npont ▴ 10
1
vote
2
replies
141
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unmatched number of reads after trimming treatment by afterqc
NGS genome assembly
18 hours ago by 德水 • 0
0
votes
1
reply
125
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq deeptools
updated 1 day ago by 152k • written 1 day ago by • 0
0
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0
replies
88
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check vsiRNA expression of mosquito (smallRNA seq data)
seq expression data smallRNA mosquito vsiRNA
1 day ago by ZuelTech • 0
0
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11
replies
352
views
Error Correction with Tadpole and BBMerge
BBmerge tadpole error correction
1 day ago by Jon • 0
2
votes
1
reply
122
views
Quantification for small RNAseq data
quantification seq data smallRNA
updated 1 day ago by ★ 1.6k • written 1 day ago by • 0
3
votes
3
replies
190
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GrCh37 or GrCh38? That is the question.
GrCh37 sequence human genome GrCh38
updated 1 day ago by 166k • written 1 day ago by ▴ 840
0
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2
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370
views
Scvi - Integration
integration singlecell scvi
5 hours ago by t.foskolos • 0
4
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3
replies
259
views
Bootstrapping in RNA-seq
bootstrapping RNAseq
updated 1 day ago by ★ 1.6k • written 2 days ago by • 0
0
votes
1
reply
213
views
Computing ka/ks ratio for individual genes.
ks ka evolution selection
updated 2 days ago by ★ 1.6k • written 3 days ago by • 0
0
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0
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214
views
Job: Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
Sweden SciLifeLab Genomics Uppsala Proteomics
4 hours ago by Matthias Zepper 5.1k
2
votes
2
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169
views
Obtaining a BED/GTF from Ensembl
rna-seq ensembl bcftools rna
2 days ago by joe_genome ▴ 60
0
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0
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120
views
News: New Bioconductor and Physalia Collaboration!
Bioconductor DataAnalysis Genomics
2 days ago by Physalia-courses ★ 2.6k
1
vote
1
reply
216
views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded STAR RNAseq antisense sense
updated 2 days ago by ★ 1.6k • written 3 days ago by ▴ 10
0
votes
1
reply
205
views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling. rnaseq gatk
updated 2 days ago by ★ 1.6k • written 3 days ago by • 0
0
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0
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119
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS covariates
2 days ago by yu • 0
5
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6
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494
views
Venn Diagram
VennDiagram
updated 1 day ago by 15k • written 5 days ago by • 0
0
votes
1
reply
168
views
PhageTerm error
phage genome phageterm assamble
updated 2 days ago by 152k • written 2 days ago by • 0
0
votes
1
reply
159
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WGCNA Workflow from GEO FASTQ Files – Expression Type, Sample Inclusion, and Preprocessing
fastq wgcna rna
updated 2 days ago by 152k • written 2 days ago by • 0
0
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0
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127
views
small RNA-Seq pipeline Standstill
NGS miRNA
2 days ago by anthony.santana.703.j ▴ 30
2
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3
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259
views
comparison interpretation
model design contrast matrix
1 day ago by jkim ▴ 200
0
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0
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130
views
piRNAs Analysis Pipelines
piRNAs smallRNA
2 days ago by GA • 0
1
vote
1
reply
171
views
Beagle PATH (partially) recognised on Ubuntu 22.04
Ubuntu Beagle Beast MCMC
updated 2 days ago by 152k • written 2 days ago by ▴ 10
0
votes
0
replies
151
views
CNV Computation with HoneyBadger
CNV HoneyBADGER
updated 2 days ago by 152k • written 3 days ago by • 0
0
votes
0
replies
148
views
How to predict programatically TFBS and calculate PWM Score as JASPAR
PWMScan TFBS JASPAR
3 days ago by t.kajiyama • 0
0
votes
0
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372
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News: Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop RNA-Seq Illumina VariantCalling DNA-Seq
3 days ago by ecSeq Bioinformatics ▴ 20
0
votes
14
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672
views
Host Removal Issues Human/Dog with samples containing Eukaryotic species
Eukarotic Mapping Host
updated 3 days ago by ★ 29k • written 4 days ago by • 0
1
vote
1
reply
250
views
Pharokka Error
error annotating viral pharokka genome
updated 3 days ago by ★ 29k • written 3 days ago by • 0
0
votes
0
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171
views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics reference-based Metatranscriptomics alignment
updated 3 days ago by 152k • written 3 days ago by • 0
1
vote
1
reply
243
views
how to make a circular plot of variants
circular plot
updated 4 days ago by 166k • written 4 days ago by ▴ 70
2
votes
6
replies
417
views
GSEA analysis
RNA-seq RNA analysis
updated 4 days ago by 152k • written 4 days ago by • 0
0
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0
replies
171
views
how to make go term plot and kegg pathway plot using InterProScan output
interproscan
4 days ago by analyst ▴ 70
1
vote
3
replies
542
views
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
mRNA rna-seq bowtie alignment
updated 4 days ago by 15k • written 5 days ago by ▴ 250
0
votes
1
reply
258
views
Questions about sample_accession_id and file_accession_id from EGA files
EGA open WGS data
updated 5 days ago by 152k • written 5 days ago by ▴ 20
4
votes
3
replies
395
views
Example of ClinVar pathogenic variant where the reference allele is pathogenic?
snp variant pathogenic clinvar
updated 5 days ago by 152k • written 5 days ago by ▴ 60
0
votes
1
reply
278
views
Functional Analysis Using EMU Output – Has Anyone Tried This?
emu
updated 5 days ago by 3.9k • written 5 days ago by • 0
1
vote
3
replies
354
views
featureCounts -t option not working in v2.0.8?
subread featureCounts RNAseq
updated 1 day ago by ★ 1.6k • written 5 days ago by • 0
121,459 results • Page 1 of 2430
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Answer: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m
Comment: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m
Answer: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m
A: Comparing metrics of two exome: how to interpret higher median coverage but lowe
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
Answer: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
Answer: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
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Recent Replies
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit by ATpoint 88k
I think I answered all of that already, also, read the manual to get code right. I am not planning to reiterate what I said already.
Comment: Interactive UMAP scanpy by antonioggsousa 3.4k
I think you should be able to use `plotly` ([docs](https://plotly.com/python/)). The UMAP plot is just a scatter plot. I think it should be…
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit by Sumeet ▴ 10
Hi @atpoint and @iansudbery Thank you for the helpful explanation, I really appreciate the clarity. Following up: I used removeBatchEf…
Comment: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m by ATpoint 88k
It's called `duplicateCorrelation` ;-)
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit by Sumeet ▴ 10
Hi Ian, Thank you for your response.
Answer: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m by i.sudbery 21k
This is an example of what the edgeR manual refers to as a "with and between" design. See page 44 of the edgeR user's guide here: https://…
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit by i.sudbery 21k
TLDR: You don't need to run removeBatchEffects, because voom will automatically remove the batch effects if you tell it about them.
Comment: Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value) by Basti ★ 2.1k
Thank you for your pertinent answer. Indeed probably I did not give a good example as screening other regions, the problem does not appear …
Answer: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit by ATpoint 88k
This has been asked many times before. If you browse support.bioconductor.org you find plenty of posts from the limma authors duscussing th…
Comment: Scvi - Integration by t.foskolos • 0
Thank for the response. I will try this one because the full dataset don't give amazing results.
Comment: Log2FC track Visualization in IGV by SomeOne ▴ 220
So as per my understanding and alot of back and forth Q&A with chatGPT this is what i found 1. If you have biological replicates then it…
Comment: FeatureCount : Successfully assigned alignments is low by HarperReed • 0
thank you very much
Comment: FeatureCount : Successfully assigned alignments is low by HarperReed • 0
yes I tried it's low
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls by Cristina • 0
Thanks so much for your response. I had assumed I could test main effects and interactions directly, but now I see how including an interac…
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls by Cristina • 0
Thank you so much for the clarification! I hadn’t understood that when I read about the design. With the interaction term, the main effects…
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