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596
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SVA correction reduces ability to detect genes as differential expressed?
gene-expression SVA RNA-seq batch-effect
updated 15 months ago by 45k • written 2.7 years ago by ▴ 60
0
votes
7
replies
3.5k
views
CoveragePlot in Signac from MACS2 Object
Signac scATAC-seq
updated 2.7 years ago by 11k • written 2.7 years ago by ▴ 30
1
vote
1
reply
746
views
Looking for RNA-seq aligner that can identify not properly mapped paired
aligner paire-end rna-seq
updated 2.7 years ago by 5.1k • written 2.7 years ago by ▴ 90
0
votes
3
replies
2.0k
views
News: NCBI update complete. Aspera users please update your client.
NCBI Submissions GenBank
2.7 years ago by PeterC_NCBI ▴ 520
0
votes
1
reply
769
views
Remove duplicates in multifasta, where entries are paired
bash python
updated 2.7 years ago by ★ 3.1k • written 2.7 years ago by ▴ 170
1
vote
3
replies
1.3k
views
'SyntaxError': 'return' outside function?
biopython pattern python regex
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
3
votes
3
replies
1.8k
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 2.7 years ago by ★ 2.1k • written 2.7 years ago by • 0
0
votes
1
reply
1.2k
views
How to remove from BAM file header all chromosomes, except chrM
samtools
updated 2.3 years ago by 45k • written 2.7 years ago by ▴ 750
0
votes
0
replies
489
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq deseq2 ampliseq ion-torrent R
2.7 years ago by Fernando • 0
0
votes
0
replies
439
views
Combining mRNA and total RNA studies
RNA-Seq bulk
updated 2.7 years ago by 45k • written 2.7 years ago by • 0
6
votes
5
replies
2.1k
views
DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS)
methylation Prediction DNA WGS WGBS Imputation
2.7 years ago by Lalaland ▴ 40
0
votes
0
replies
1.2k
views
Job: Computer scientist / Bioinformatician
data-science software-development structural-bioinformatics machine-learning
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Define and set up Standards curve
quantstudio qPCR qpcr
updated 2.7 years ago by 5.1k • written 2.7 years ago by ▴ 40
0
votes
0
replies
548
views
Bootstrap in PhyML
phyml bootstrap
2.7 years ago by Jimpix ▴ 10
0
votes
0
replies
1.2k
views
Enrichment map in python/ Pathway network by using python
network pathway-enrichment interaction
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
TCGAbiolinks HT-Seq count
HT-Seq TCGAbiolinks
updated 2.6 years ago by 45k • written 2.7 years ago by ▴ 10
0
votes
1
reply
867
views
How to analysis genomes with orthologs?
ortholog genome annotation
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
1
vote
2
replies
5.2k
views
VCF to Plink files
vcf pink pgen psam
2.7 years ago by hi.there • 0
0
votes
0
replies
426
views
Does the falcon input CLR reads need corrected by Canu?
Genome assemble
2.7 years ago by leeunfeng • 0
3
votes
2
replies
5.8k
views
Heatmap by group in R
ggplot2 R heatmap
updated 2.7 years ago by ▴ 370 • written 2.7 years ago by ▴ 50
0
votes
0
replies
936
views
CUT&RUN H3K27me3 normalization with spike-in
deepTools
2.7 years ago by mohansri1 • 0
14
votes
9
replies
2.9k
views
Scientific Notation to Decimal
notation decimal scientific
2.7 years ago by am29 ▴ 60
4
votes
4
replies
2.1k
views
A way to get a list of determined and undetermined indexes using illumina interop library?
interop python illumina
updated 2.7 years ago by 154k • written 2.7 years ago by ▴ 30
2
votes
2
replies
5.3k
views
IGV resizing tracks
IGV
updated 2.7 years ago by ▴ 10 • written 9.5 years ago by ★ 3.6k
0
votes
2
replies
955
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 2.7 years ago by 5.1k • written 2.7 years ago by ▴ 140
0
votes
3
replies
1.6k
views
Change accession number to chromosome number in reference genome
fasta chromosome
updated 2.7 years ago by 45k • written 2.7 years ago by • 0
1
vote
1
reply
3.5k
views
Aspera: Command 'ascp' not found
aspera linux idr ssh
updated 2.7 years ago by 89k • written 2.7 years ago by • 0
0
votes
0
replies
487
views
Median depth across samples from multi-sample VCF
bcftools
updated 2.3 years ago by 45k • written 2.7 years ago by • 0
0
votes
4
replies
2.6k
views
NMDS: how many axes to plot?
NMDS
2.7 years ago by LaFra ▴ 10
0
votes
5
replies
1.4k
views
Add Information to Protein Fasta Headers
protein fasta functional-annotation header
2.7 years ago by ahmadjoyyia ▴ 30
5
votes
2
replies
2.3k
views
WGCNA gene selection: gene significance or LASSO?
LASSO WGCNA
updated 2.7 years ago by 13k • written 2.7 years ago by ▴ 10
0
votes
0
replies
746
views
why count_matrix.csv generated by "prepDE.py3" showed unidentified IDs
Stringtie RNA-seq
2.7 years ago by Pegasus ▴ 130
1
vote
3
replies
1.9k
views
Single sample GSEA analysis
single sample
updated 2.7 years ago by ★ 1.9k • written 2.7 years ago by ▴ 130
2
votes
3
replies
1.2k
views
biological vs. technical definition of "insert size"
grinder simulated-reads shotgun-sequencing
updated 2.7 years ago by 89k • written 2.7 years ago by ▴ 100
0
votes
0
replies
704
views
Haloplex HS - should you remove duplicates?
deduplicate Haloplex duplicates
2.7 years ago by amy__ ▴ 250
3
votes
4
replies
1.4k
views
RNAseq: Scaling or not scaling with rlog transformed counts
scale rlog RNAseq clustering DESeq2
2.7 years ago by Laurie • 0
0
votes
0
replies
601
views
Interpreting SnpEff output plots
NGS Annotation SnpEff WGS WES
2.7 years ago by Alireza ▴ 30
0
votes
0
replies
713
views
Using DANPOS2 to determine nucleosome positions
MNase-seq DANPOS ENCODE bigwig
2.7 years ago by elisheva ▴ 120
3
votes
7
replies
1.8k
views
How to change every third line in a fastq library
fastq
updated 2.7 years ago by 45k • written 2.7 years ago by • 0
0
votes
0
replies
497
views
How to determine the receptor and binding site of a protein transcribed from a gene
gene
2.7 years ago by yoser4 ▴ 10
0
votes
4
replies
2.4k
views
blast engine error empty blast query vector
Blast alignment
updated 2.4 years ago by 45k • written 2.7 years ago by ▴ 70
0
votes
0
replies
513
views
WGCNA Error in moduleEigengenes: setting key from pcagrey to pcagrey_
wgcna
2.7 years ago by 瀚 • 0
0
votes
0
replies
491
views
Exon 1 coverage of ADAMTS2 gene
WGS Coverage
2.7 years ago by RK • 0
0
votes
0
replies
697
views
bcftools error: bcftools could not parse pval threshold loidly
bcftools mpileup
2.7 years ago by mut.patricia ▴ 20
0
votes
0
replies
600
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression miRNA correlation
2.7 years ago by Zahra ▴ 110
0
votes
2
replies
1.0k
views
No variants found ( have problem in the handbook)
bcftools biostar-handbook variant-calling igv
updated 2.3 years ago by 45k • written 2.7 years ago by • 0
4
votes
3
replies
2.2k
views
gff file from NCBI RefSeq GCF dataset has an invalid format
NCBI gff
2.7 years ago by Michael • 0
1
vote
2
replies
1.2k
views
How can I best sequence T and B cells for the sequence of their receptors?
scRNASeq B-cells
updated 2.7 years ago by ▴ 60 • written 3.6 years ago by • 0
0
votes
0
replies
586
views
Anti-CRISPR and Cas protein interactions
crispr anti-crispr proteins
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
0
votes
0
replies
1.1k
views
issues with amber_minimize.py failing to use CUDA within alphafold
linux CUDA amber alphafold
2.7 years ago by charlieclark1ee ▴ 20
122,021 results • Page 305 of 2441
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Answer: Scientific Names In Blast Output And Databases
Answer: Scientific Names In Blast Output And Databases
Scientific Names In Blast Output And Databases
Answer: 1 vs 1 DEG analysis in scrna seq data
Answer: samtools 1.0 'index' : CSI index vs BAI index ?
Answer: samtools 1.0 'index' : CSI index vs BAI index ?
samtools 1.0 'index' : CSI index vs BAI index ?
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Answer: What is the length of the longest ORF appearing in reading frame 2 of any of the by fra.r.silvestro ▴ 10
I suppose that this is a good resolution: frame = 2 protein_seq_frame2 = sequence[frame -1:] protein_seq_frame3 = protein…
Comment: HDOCK Server Error! by GenoMax 154k
This could be caused by the line endings that differ between macOS and Windows. Generally a utility like `dos2unix` can help fix this. You …
Comment: What is the length of the longest ORF appearing in reading frame 2 of any of the by Mensur Dlakic ★ 30k
Generally speaking, we are not here to provide code review service and/or fix code for what appears to be a school assignment. If you have …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Istvan Albert 103k
We don't have 6 minutes to watch something without even knowing what it does. I would recommend that you provide a brief explanation of wh…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Yang • 0
Thanks for the reply, I simply recorded the screen and used brave to integrate fastqc analysis. You can click the link below to view. In ge…
Answer: Variant Normalization by Istvan Albert 103k
The purpose of normalization is to ensure that identical variants are represented identically. When not normalized, the same variants may …
Answer: Should differential expression analysis be incorporated in cross validation for by i.sudbery 22k
Yes, their would potentially be data leakage if you perform the DE before dividing your datasets into folds. Its unclear how much of a prob…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Istvan Albert 103k
I visited the website, but I couldn't understand what problem the software solves. You need to do a much better job of communicating the p…
Comment: Choosing enrichment analysis tool by i.sudbery 22k
How have these gene lists been obtained?
Comment: NOVOPlasty assembly fails with “INVALID SEED” using first read as seed by GenoMax 154k
> I used the first read sequence from ERR322446.filtered.A.fq as the seed `ERR322446` appears to be a human sample. Did you convert the …
Answer: Issue with Snippy 4.6.0 by GenoMax 154k
> Each individual Snippy run completes successfully and reports multiple variants When you run `snippy-core` there is no reference provid…
Comment: Quantification using salmon in alignment-based mode after minimap2 run by Assa Yeroslaviz ★ 1.9k
Hi Rob, sorry for the late question. I was wondering though, if I can also quantify transposable elements using oarfish? Should I increas…
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.
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