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122,008 results • Page 275 of 2441
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608
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How to normalise ChIP-Seq samples using deeptools
bamCoverage deepTools
updated 2.3 years ago by 45k • written 2.5 years ago by ★ 1.9k
1
vote
2
replies
1.2k
views
R script error R aborted or encountered a fatal error
linux R
updated 2.5 years ago by 4.2k • written 2.5 years ago by ▴ 30
0
votes
2
replies
1.5k
views
How do I call all the variants with BCFTOOLS?
bcftools variant-calling
2.5 years ago by stefania.morelli92 • 0
4
votes
3
replies
1.7k
views
Testing overlap significance of three gene sets using the hypergeometric distribution
Hypergeometric-distribution gene-sets
2.5 years ago by Pac314 ▴ 10
27
votes
21
replies
47k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 24 months ago by ▴ 80 • written 11.3 years ago by ▴ 170
2
votes
2
replies
1.1k
views
Illumina simulated reads - tools or SRA projects
metagenomics simulated simulator illumina reads
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 10
7
votes
5
replies
2.0k
views
RNA-seq analysis without replicates
DGE RNA-seq GSEA
updated 2.5 years ago by ▴ 150 • written 2.5 years ago by ▴ 90
0
votes
1
reply
900
views
"align" in rsubread only reading 1 out of 6 of my input files
rnaseq rsubread align
updated 2.5 years ago by 154k • written 2.5 years ago by • 0
0
votes
0
replies
587
views
Couldn't get proper result when using merfin for T2T polish
medaka merfin assemble polish T2T
2.5 years ago by 2668428466 • 0
3
votes
5
replies
2.2k
views
How do I convert GUI operations to CUI operations in pymol?
pymol pdb
updated 2.5 years ago by ★ 2.1k • written 2.6 years ago by ▴ 10
8
votes
6
replies
1.7k
views
How to "guess" the transformation based on already-transformed, "normalized count data"?
edger rnaseq rna rna-seq
2.5 years ago by wangziwei0010 ▴ 30
2
votes
1
reply
802
views
I need a tool that allows me to see a whole genome and point out previously annotated genes
genomeviewer genomics wgs
updated 2.5 years ago by 8.7k • written 2.5 years ago by • 0
0
votes
1
reply
764
views
Tool to calculate per-nucleotide confidence score in genome assembly using short-read data
quality score genome assembly
updated 2.5 years ago by ▴ 660 • written 2.5 years ago by ▴ 10
2
votes
2
replies
973
views
How to blast multiple sequences against one database at once? (command line)
unix blast
2.5 years ago by M. ▴ 40
2
votes
6
replies
3.2k
views
Need help with Velocyto Analysis. Errors: MemoryError: bam file #0 could not be sorted by cells.
10xgenomics velocyto RNA velocity
2.5 years ago by Anna ▴ 20
1
vote
3
replies
2.1k
views
How to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene symbol in NCBI gene with R?
Transcription-start-site R biomart
updated 2.5 years ago by 4.7k • written 2.5 years ago by ▴ 110
0
votes
2
replies
1.0k
views
Deseq2/ComplexHeatmap - is it possible to combine 4 heatmaps together?
deseq2 rnaseq map heat
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 10
4
votes
4
replies
5.6k
views
Merging more than 2 csv files in R
merge r
updated 2.5 years ago by 12k • written 9.6 years ago by • 0
0
votes
0
replies
753
views
Small overlap of 1KG Sample file with dbSNP and same sample from phased file
HaploTypeCaller 1KG dbSNP
2.5 years ago by berndmann ▴ 10
1
vote
1
reply
1.6k
views
phyloseq error
phyloseq
updated 2.5 years ago by ▴ 420 • written 2.5 years ago by • 0
1
vote
4
replies
1.1k
views
how to deal with "The number of covariates exceeds the number of samples" on matrixeqtl
covariate matrixeqtl
2.5 years ago by Binghong ▴ 20
0
votes
0
replies
548
views
Are any recommended tools to deal with many missing values in the phospho proteomics data matrix
limma phosphoproteomics
2.5 years ago by alwayshope ▴ 40
3
votes
8
replies
2.0k
views
sorting and moving a bunch of fasta files into separate folder
fasta bash
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
3
votes
2
replies
1.2k
views
'closure' is not subsettable error in r shiny
shiny R
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
5
votes
6
replies
1.4k
views
normalize coordinates to the same length
r genomicranges
2.5 years ago by Chironex ▴ 50
0
votes
3
replies
1.0k
views
How to predict the mature miRNA from its precursor
RNAfold microrna
updated 2.5 years ago by 8.0k • written 2.5 years ago by • 0
0
votes
0
replies
540
views
Simulation of pathways in scRNA
scRNA simulation pathways
2.5 years ago by sp29 ▴ 50
1
vote
2
replies
991
views
Shortest scaffold
platanus scaffolding
2.5 years ago by Takuma ▴ 20
0
votes
0
replies
686
views
retrieve peaks associated to a gene SIGNAC
single-cell seurat r signac
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 50
0
votes
0
replies
592
views
Regression coefficient for downstream analysis from lasso regression for survival analysis
Survival
2.5 years ago by 1769mkc ★ 1.3k
0
votes
3
replies
1.3k
views
delly filter input file
delly
updated 2.2 years ago by 45k • written 2.5 years ago by • 0
1
vote
5
replies
2.4k
views
GFF/GTF file error / featureCounts
RNA-SEQ
updated 2.5 years ago by ★ 2.5k • written 2.5 years ago by ▴ 130
0
votes
0
replies
449
views
Count Number and Length of RAD Contigs in VCF file
vcf
2.5 years ago by Zoe • 0
3
votes
1
reply
1.2k
views
How to Merge RNA Replicates
EdgeR FPKM RNA counts
updated 2.5 years ago by ★ 8.3k • written 2.5 years ago by ▴ 110
1
vote
3
replies
1.9k
views
Is it possible to draw volcano plot without p values
p-value log2fold plot
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 140
4
votes
6
replies
2.7k
views
remove batch effect
harmony
updated 2.0 years ago by ▴ 260 • written 2.5 years ago by ▴ 120
1
vote
1
reply
2.5k
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 22 months ago by ▴ 10 • written 2.5 years ago by ▴ 360
1
vote
11
replies
2.7k
views
MultiQC output: opposing output
cutadapt fastqc multiQC genotype-by-sequencing GBS
updated 2.5 years ago by ★ 1.5k • written 2.5 years ago by ▴ 10
0
votes
1
reply
739
views
BAM Similarity
bam
updated 2.5 years ago by 154k • written 2.5 years ago by • 0
2
votes
2
replies
844
views
Problem using efetch -format acc, not the right accessions returned
efetch esearch edirect entrez
2.5 years ago by Lei ▴ 20
0
votes
0
replies
652
views
scATAC integration
scatac-seq integration
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 30
2
votes
3
replies
1.4k
views
Why can’t we have full-length transcripts with droplet-based technologies ?
single-cell UMI smart-seq3
2.5 years ago by sagane.joye • 0
3
votes
6
replies
1.7k
views
Seqtk
seqtk
2.5 years ago by bestone ▴ 30
0
votes
0
replies
564
views
Any tools for systematic downstream enrichment analysis/comparison
enrichment downtream RNAseq
2.5 years ago by alwayshope ▴ 40
5
votes
11
replies
3.7k
views
Diffbind dba.count doesn't give FRiP score
Diffbind FRiP
updated 2.3 years ago by ★ 2.1k • written 2.5 years ago by • 0
0
votes
0
replies
7.4k
views
Forum: Optimal approach for variant calling with 3 diluted germline sample in one sequencing - Capture Sequencing
germline Calling Variant Capture Sequencing
2.5 years ago by Alexandre Eeckhoutte • 0
0
votes
1
reply
993
views
Getting chromosome of unusual chromosome names e.g. 'CHR_HSCHR8_8_CTG1'
chromsome biomart
2.5 years ago by 4galaxy77 2.9k
1
vote
1
reply
1.0k
views
Zero lifted variants with Picard, CrossMap and bcftools liftover
bcftools liftover
2.5 years ago by Sumaya • 0
0
votes
1
reply
949
views
Plink Meta-Analysis Query
Meta-Analysis GWAS Plink
updated 2.5 years ago by ▴ 130 • written 2.5 years ago by • 0
2
votes
3
replies
758
views
Regression factor levels question
logistic-regression snp
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
122,008 results • Page 275 of 2441
Recent Votes
Comment: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
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Recent Replies
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts by andres.firrincieli 3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
Answer: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
(I apologise for my previous reply; I wanted to be as detailed as possible) DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I apologise for how that sounded; I wanted to be as detailed as possible.
Comment: GUI commercial software for 10x single cell gene expression analysis by Istvan Albert 103k
A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by GenoMax 154k
> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
Answer: FACS quality control based on size and doublet detection in scRNA-seq by ATpoint 89k
No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Apparently you are working with human proteins? I would strongly recommend looking only at proteins that are part of the human reference pr…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by colindaven 8.0k
Wow, thats too long. How much RAM does your machine have, it is likely swapping
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
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