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122,013 results • Page 599 of 2441
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3
votes
5
replies
1.8k
views
Downloading WGBS sequencing reads for cancer sample and healthy sample
Dataset Cancer WGBS Healthy
4.1 years ago by Nishat ▴ 10
0
votes
0
replies
1.3k
views
Job: Bioinformatician/Computational Biologist. Single cell genomics of primate brain to design cell-type-targeted viral vectors. 2 positions, Basel Switze…
AAV single-cell brain epigenomics
updated 2.3 years ago by 45k • written 4.2 years ago by ▴ 50
5
votes
5
replies
2.0k
views
Direct - indirect binding of a transcription factor in chip-seq analysis
directbinding indirectbinding trancriptionfactors chipseq chipseqanalysis
updated 4.2 years ago by ▴ 520 • written 4.2 years ago by ▴ 130
2
votes
7
replies
1.2k
views
How can I get the exact 3D structure of the protein to use the PDB file for PPI docking
Uncharacterized Protein structure
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
3
votes
4
replies
6.3k
views
library(Seurat) shows error: package or namespace load failed for ‘Seurat’ in .doLoadActions(where, attach)
Seurat
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
0
votes
0
replies
543
views
Multi-phenotype GWAS analysis, how to deal with high lambda
statistics GWAS
4.2 years ago by Miranda • 0
1
vote
2
replies
2.0k
views
Error in DESeqDataSetFromMatrix Function in DESeq Library
Differential Gene DESeq R Expression
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 50
0
votes
0
replies
531
views
PMut server error
PMut
updated 15 months ago by 45k • written 4.2 years ago by • 0
0
votes
4
replies
2.3k
views
Best match Blast
tblastx
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 10
2
votes
11
replies
10k
views
Alignment using bwa-mem2
alignment bwa-mem2
4.2 years ago by priya.bmg ▴ 70
4
votes
7
replies
2.0k
views
The usage of sed
linux sed shell
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
0
votes
0
replies
675
views
Bioinformatic interrogation of non-coding variants in gVCFs
VCF gVCF non-coding
4.2 years ago by tacrolimus ▴ 150
0
votes
0
replies
368
views
Library normalization of data sets containing RFUs?
somascan
4.2 years ago by Ina Jungersen • 0
1
vote
3
replies
2.3k
views
Read group info
info read BWA group bwa-mem2
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 70
3
votes
5
replies
2.0k
views
Where do I get a WES dataset of size <1GB
WGS WES genomics
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 10
3
votes
5
replies
18k
views
NCBI error report
blastp alignment
updated 2.3 years ago by 45k • written 9.6 years ago by ▴ 210
0
votes
1
reply
854
views
SRA splitting for each metagenome-assembled genome
SRA metagenome-assembled metagenome genome MAG splitting
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
4
votes
8
replies
5.0k
views
8 follow
R Programming - how to make a simple heat map
Heatmap R
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
0
votes
1
reply
1.4k
views
question about running CIRI-full
RNA-Seq
updated 4.2 years ago by • 0 • written 5.5 years ago by • 0
2
votes
2
replies
1.9k
views
How to identify mutations from FASTA sequences?
Mutation Fasta
updated 4.2 years ago by ▴ 20 • written 4.2 years ago by ▴ 80
0
votes
7
replies
2.4k
views
align using file.ht2
ht2 hisat2
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 30
0
votes
2
replies
4.2k
views
Export normalized matrix Scanpy
Scanpy
updated 4.2 years ago by ★ 1.7k • written 4.2 years ago by • 0
0
votes
0
replies
1.6k
views
Job: JOB OPPORTUNITY!!! Scientist, Next Generation Sequencing (Molecular Biology)
NGS careers
updated 2.4 years ago by 45k • written 4.2 years ago by • 0
2
votes
2
replies
1.4k
views
Samtools difference between Mapped and Unmapped read
unmapped samtools mapped
updated 4.2 years ago by 48k • written 4.2 years ago by • 0
0
votes
3
replies
1.4k
views
DESeq2 design question
RNA-seq DESeq2 R
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by ▴ 30
1
vote
2
replies
1.2k
views
How to find the number of copies of genes (e.g. 23S rRNA) present in a genome?
antimicrobial-resistance reference-database copies-of-genes metadata NCBI
4.2 years ago by eli_bayat ▴ 100
0
votes
0
replies
623
views
Performing enrichment analysis using extracted GOs from topGO
analysis enrichment topGo Enrichment Functional
4.2 years ago by KennedyOmufwoko • 0
0
votes
2
replies
919
views
I can't find T cell receptors in my RNAseq expression table
TRDC t-cell NGS TRBC2 TRAC
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 20
0
votes
2
replies
3.9k
views
gatk4 python package
conda package python gatk4
4.2 years ago by Mehmet ▴ 820
2
votes
7
replies
3.7k
views
How do I log into this ftp server and look around?
ftp
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 900
4
votes
5
replies
2.8k
views
Copy number differences between groups
CNA Differential GISTIC
updated 4.2 years ago by • 0 • written 7.1 years ago by ▴ 50
1
vote
4
replies
5.1k
views
how to Seurat::RunUMAP() but run reduction="pca" on subset of features?
seurat pca umap
4.2 years ago by mk ▴ 310
1
vote
5
replies
6.6k
views
seurat `<obj>@assays$RNA@counts` vs `<obj>@assays$RNA@data`?
seurat
updated 4.2 years ago by 13k • written 4.2 years ago by ▴ 310
1
vote
2
replies
1.3k
views
Low assignment rate with featureCounts
featureCounts RNA-seq STAR
4.2 years ago by gt ▴ 30
6
votes
8
replies
3.9k
views
k-mer counters - presence/absence matrix
k-mers matrix
4.2 years ago by lizabe ▴ 10
0
votes
0
replies
1.1k
views
Error while subsetting VCF - error doesn't check out with (z)grep
bcftools vcf
4.2 years ago by Ram 45k
0
votes
0
replies
1.7k
views
EOF marker absent in VCF - can this be safely ignored?
bcftools VCF EOF
4.2 years ago by Ram 45k
0
votes
0
replies
690
views
Job: Staff Scientist and Engineering positions at Scripps Research (San Diego CA or remote)
infectious-diseases data-visualization
updated 3.2 years ago by 45k • written 4.2 years ago by • 0
1
vote
2
replies
1.7k
views
Differential gene expression: remove effect of latent variables from log fold change
Seurat scRNA-seq genomics
4.2 years ago by danielcgingerich ▴ 10
1
vote
5
replies
1.6k
views
Local blast database
database update_blastdb.pl blast
4.2 years ago by Vasiliy Krestov ▴ 30
2
votes
2
replies
2.3k
views
blastx versus tblastx
tblastx blastx
4.2 years ago by aka ▴ 10
4
votes
4
replies
2.5k
views
Trimming of adapters and indexes
NGS small-DNA trimming trimmomatic sequencing
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 30
1
vote
2
replies
1.1k
views
Pooling annotations from different databases in InterProScan
annotations interproscan protein sequence domain
4.2 years ago by Dunois ★ 2.9k
2
votes
2
replies
1.2k
views
What Galaxy tools add Ns to variable length FASTQ sequences to get uniform length? (FASTA if needed)
length galaxy fastq ngs
updated 4.2 years ago by 23k • written 4.2 years ago by ▴ 20
0
votes
10
replies
2.5k
views
DESeq2 analysis result differences
patch-seq RNA-Seq DESeq2 Dropouts
4.1 years ago by pkallurkar • 0
0
votes
2
replies
3.4k
views
Help with finding p value comparing 3 groups with different n
p-value
updated 4.2 years ago by ▴ 60 • written 4.2 years ago by • 0
0
votes
1
reply
1.2k
views
some values in assay are negative
deseq2
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
1
reply
1.8k
views
Problems with fragment length distribution output with Salmon
distribution Salmon RNA-Seq fragment length multiqc
updated 4.2 years ago by 4.2k • written 4.2 years ago by • 0
0
votes
2
replies
1.4k
views
Map Entire Directory of Paired-End Reads at Once
bwa bowtie genomics assembly reads
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.9k
views
rna-seq STAR early terminates with error message: std::out_of_range' / vector::_M_range_check when processing annotations GTF
bacteria STAR prokaryotes rna-seq
4.2 years ago by Constanza • 0
122,013 results • Page 599 of 2441
Recent Votes
Comment: Reading AD and other genotype information from the VCF file
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
The Biostar Handbook. A bioinformatics e-book for beginners.
Genome Assembly QC from BAM files
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Recent Replies
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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