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2
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1
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792
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Intersecting Wald DESeq2 Results
LRT DESeq2 Wald
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
1.3k
views
UK Biobank methylation data
DNA biobank methylation
4.4 years ago by Ivan • 0
6
votes
5
replies
1.6k
views
How to create matrix from row data
sed perl R awk
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 30
0
votes
1
reply
2.0k
views
How to interpret Enrichr combined score 'infinity' value
Enrichr Enrichment
updated 11 months ago by ▴ 100 • written 4.4 years ago by • 0
2
votes
2
replies
1.4k
views
Trouble with plotMA
plotMA DeSeq2 R
updated 3.7 years ago by 89k • written 4.4 years ago by • 0
4
votes
3
replies
2.3k
views
Normalize by contig size BEFORE RPKM normalization?
virus normalization metagenomics edgeR RPKM
updated 4.4 years ago by ★ 3.3k • written 4.4 years ago by ▴ 160
0
votes
0
replies
610
views
How does changes in pH change the conformation of a protein - Software
quaternary pH structure protein
4.4 years ago by roybatty269 • 0
1
vote
4
replies
991
views
Error in chopping alignment files for each chromosome
alignment
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
1
vote
5
replies
1.5k
views
Could someone help me check what genomic position is this variant nomenclature referring to ?
nomeclature
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 890
1
vote
0
replies
851
views
Calculating Fst from low coverage data using genotype likelihoods
vcftools fst population_differentiation
4.4 years ago by Jautis ▴ 580
0
votes
3
replies
2.6k
views
customized gene not show in the output from cellranger count even if I have added to the reference genome database
gene scRNA cellranger
updated 4.4 years ago by ▴ 40 • written 4.4 years ago by ▴ 150
0
votes
0
replies
619
views
Creating phylogenetic trees for a full genome at once?
genomic Phylogeny
4.4 years ago by blur ▴ 280
1
vote
2
replies
1.2k
views
fastq-dump for downloading multiple sets reads?
illumina ncbi fastq-dump genomes
4.4 years ago by c.e.chong ▴ 60
2
votes
11
replies
2.8k
views
Using snakemake in order to download reads and run hisat2 mapping
hisat2 snakemake python
updated 4.4 years ago by 23k • written 4.4 years ago by ▴ 140
0
votes
1
reply
718
views
Clinical Data Analysis in R for significant difference between 2 groups in R
testing Biostatistics Significant R
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
1
reply
941
views
Distance Correlation Matrix Intrepretation
statistics correlation R
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
2
votes
6
replies
2.7k
views
How can I draw this plot?
bcftools roh-calling roh samtools
updated 3.6 years ago by ▴ 350 • written 4.4 years ago by ▴ 260
2
votes
2
replies
1.2k
views
How to associate secondary structure to protein sequence
secondary python structure pdb database
4.4 years ago by francesco.costa.11 ▴ 30
1
vote
3
replies
942
views
How to find variants which are not present in second file
vcf
updated 4.4 years ago by 166k • written 4.4 years ago by ▴ 40
0
votes
2
replies
1.8k
views
HaplotypeCaller output mode
GATK HaplotypeCaller
4.4 years ago by puddingmeow516 ▴ 10
1
vote
3
replies
1.3k
views
Where to find 'nr. Non-redundant GenBank...' the peptide sequence database?
database genbank
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 20
4
votes
5
replies
4.1k
views
Varying read length distribution after running Trimmomatic
RNAseq pairedend Trimmomatic
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 140
1
vote
0
replies
805
views
News: Online Training -low-coverage Whole Genome Sequencing
Genome SNPs NGS WholeGenomeSequencing
4.4 years ago by Physalia-courses ★ 2.6k
0
votes
0
replies
717
views
News: Online Training -Generalised Linear Models in R
GLMs statistics GeneralisedLinearModels R
4.4 years ago by Physalia-courses ★ 2.6k
0
votes
5
replies
1.4k
views
conversion from genomic to gene coordinates in a large file
plink
4.4 years ago by storm1907 ▴ 30
2
votes
1
reply
1.9k
views
CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE when running guppy basecaller
basecalling ont guppy nanopore cuda
4.4 years ago by eoneill627 ▴ 20
1
vote
3
replies
1.4k
views
Assigning small RNA reads
featureCount smallRNA rna rna-seq sequencing
updated 4.4 years ago by 9.0k • written 4.4 years ago by ▴ 10
2
votes
1
reply
1.8k
views
CNVkit result interpretation
CNVkit result cns
updated 2.1 years ago by ▴ 640 • written 4.4 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Using RPKM to compare gene expression between samples
rnaseq normalization rpkm
updated 4.4 years ago by ★ 7.7k • written 4.4 years ago by • 0
1
vote
6
replies
1.6k
views
Grepping samples out of vcf and writing them to a new file
VCF grep bgzip bcftools
4.4 years ago by Kath__ ▴ 10
2
votes
6
replies
22k
views
How to explain the MA plot for differential expression analysis in RNA-seq data?
rna-sequencing graphs analysis
4.4 years ago by ashwing.kofficial ▴ 10
2
votes
1
reply
1.2k
views
Phenotype Enrichment Analysis vs Gene Enrichment Analysis
enrichment gene phenotype
updated 4.4 years ago by 56k • written 4.4 years ago by ★ 9.6k
0
votes
0
replies
440
views
Where can I find the ggKbase wrapper scripts?
ggKbase 16s.sh
4.4 years ago by Rui ▴ 50
0
votes
6
replies
3.6k
views
Microarray data analysis in R
agilent single-colour microarray
4.1 years ago by smrutimayipanda ▴ 20
0
votes
0
replies
944
views
Forum: CADD Error in EXOMISER
exomiser cadd
4.4 years ago by shwetan • 0
0
votes
1
reply
1.0k
views
Gene locations do not match
ChIP-Seq
updated 4.4 years ago by 89k • written 4.7 years ago by • 0
0
votes
3
replies
1.8k
views
Synonymous and asynonymous sites in Ka/Ks
Ka Ks
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 60
0
votes
1
reply
2.0k
views
ChIPSeeker Help for Annotating Peaks
ChIP-Seq atac-seq software error
updated 4.4 years ago by ▴ 220 • written 4.8 years ago by • 0
9
votes
4
replies
8.2k
views
How to filter out a list of specific genes from the DESeq object in R - bulk RNA-seq differential expression
R bulk object DESeq2 filter
4.4 years ago by msimmer92 ▴ 310
5
votes
7
replies
3.3k
views
EBI API GWAS query over gene
GWAS API EBI Python
updated 4.3 years ago by ▴ 30 • written 4.4 years ago by ▴ 170
4
votes
7
replies
3.3k
views
How to choose one TSS for a gene
transcription site tss start
4.4 years ago by GG • 0
3
votes
5
replies
2.5k
views
Mapping RNA seq reads from bed file to genes
RNAseq gene-expression tpm
4.4 years ago by jrose ▴ 30
0
votes
2
replies
877
views
Both mate pairs aligning to same contig counts
paired_reads samtools_coverage
4.4 years ago by Matan • 0
0
votes
0
replies
914
views
News: Call for abstracts BioSB 2021!
biosb conference dutch
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 230
1
vote
2
replies
3.0k
views
help to download Repbase repeatmasker
next-gen assembly software error
updated 4.4 years ago by ▴ 10 • written 5.0 years ago by • 0
0
votes
2
replies
1.8k
views
Why do paired ends map to same coordinates of a scaffold?
reads map magicblast SRA
4.4 years ago by wmorgan ▴ 20
0
votes
1
reply
698
views
Yeast genome annotation: How to predict genes and CDS of them?
ncbi yeast annotation
updated 2.5 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
513
views
inquiry related to docking
docking
4.4 years ago by rheab1230 ▴ 150
0
votes
3
replies
2.8k
views
demultiplex paired end fastq file with mixed samples with barcode
RNAseq fastq demultiplex
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 40
4
votes
4
replies
3.9k
views
1000G Tabix download: EOF marker is absent
1000Genomes Tabix vcf-subset bgzip
updated 4.4 years ago by 2.9k • written 4.4 years ago by ▴ 40
121,884 results • Page 665 of 2438
Recent Votes
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
Comment: Fastq reads to csv - How can I make a csv with the read number of several fastq
Answer: Fastq reads to csv - How can I make a csv with the read number of several fastq
Answer: Fastq reads to csv - How can I make a csv with the read number of several fastq
Comment: Fastq reads to csv - How can I make a csv with the read number of several fastq
Answer: How to debug faulty BBmap clumpify command?
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Recent Replies
Comment: Is this PCA plot correct?? by dthorbur ★ 3.1k
In addition to these comments, I would suggest checking other PCs, the first two PCs only explain a combined 39% of the variance. Since you…
Answer: Is this PCA plot correct?? by ATpoint 89k
Assuming that the PCA was "technically" done correctly (bulletproof way would be to use plotPCA from DESeq2 as a wrapper) -- then the separ…
Answer: Is this PCA plot correct?? by Mensur Dlakic ★ 30k
I can tell you what you already know: this result is unexpected. Nobody can tell you whether the plot is "correct" or not - it depends on w…
Answer: Strange pattern in pct_counts_mt from bin2cell deconvolved VisiumHD data by danielpintard ▴ 10
Update: take a look at the plot below ![enter image description here][1] [1]: /media/images/2a939635-9920-46b9-9b15-6028022d
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
Experiments with global changes in the RNA production usually need spike-in normalization to estimate the library sizes. Questions about th…
Comment: Best way to do protein structure guided similarity search? by Dunois ★ 2.9k
`Foldseek` perhaps? They have a server for it too: [https://search.foldseek.com/][1] . [1]: https://search.foldseek.com/
Comment: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates by GenoMax 153k
As of Sept 2025 this script is coded only for human gene symbol lookups as noted on GitHub page, with a promise to make it flexible later.
Comment: How to debug faulty BBmap clumpify command? by GenoMax 153k
> worked flawlessly on another machine If you rearranged/moved the contents of BBMap software bundle from default, it can lead to the "cla…
Answer: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates by Thanujay S • 0
Hey! A bit late to the party! I’ve built a simple wrapper (named SESC) around biomaRt to streamline Ensembl ID conversions. It supports bo…
Comment: How to debug faulty BBmap clumpify command? by marongiu.luigi ▴ 760
It makes sense since the command worked flawlessly on another machine... Thanks
Comment: Finding RNA genes associated with X protein expression in CITE-seq Seurat object by ATpoint 89k
One way would be to make a correlation test between every pair of gene-ADT, and test for significance. Another would be to run something li…
Answer: How to debug faulty BBmap clumpify command? by Matthias Zepper 5.1k
It is trying to access the BBTools `sketch` tool that is a dependency and doesn't find it. I have almost no experience with Java, but m…
Comment: [vg giraffe] Unable to add read group to BAM file by saruman • 0
The read alignment does not produce any error. The BAM file does not include the read group. I need to run `picard AddOrReplaceReadGroups` …
Comment: Best way to do protein structure guided similarity search? by lieven.sterck 15k
Something along the line of working with HMMs: you could also consider using PSI-BLAST. (though equally non-modern like HMM searches :) )
Comment: Best way to do protein structure guided similarity search? by Joe 22k
There are tools that sort of do this with sequence information still. I would consider looking at HMM based methods for starters (`hhsuite…
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