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144 results • Page 1 of 3
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QC exclusion of A/T or G/C alleles to avoid strand issues
SNP QC quality control SNV
just now by _quantum_girl_ ▴ 10
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6
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traying to make a maf from an already annotated vcf
vcf2maf VEP maftools
updated 11 minutes ago by 43k • written 14 minutes ago by • 0
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0
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13
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Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
33 minutes ago by enferdeflame • 0
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0
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12
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Difference when using difference number of pathways score to compare between 3 groups
Limma GSVA
29 minutes ago by Chris ▴ 260
0
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1
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343
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How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 50 minutes ago by 43k • written 19 months ago by • 0
0
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2
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173
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RNA seq differential expression analysis
RNA-seq normalization
updated 57 minutes ago by 43k • written 6 hours ago by • 0
0
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1
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120
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How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
updated 2 hours ago by 141k • written 6 hours ago by ▴ 20
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54
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How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 56 minutes ago by 43k • written 7 hours ago by ▴ 10
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0
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66
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How to root an unrooted tree with a known root tree?
phylogenetics rooting R
7 hours ago by P. • 0
0
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0
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69
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Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
9 hours ago by ekirsch • 0
0
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0
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99
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Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
14 hours ago by renan.igor • 0
0
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0
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89
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filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
16 hours ago by synat.keam ▴ 100
0
votes
1
reply
177
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assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 18 hours ago by 141k • written 18 hours ago by • 0
0
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2
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253
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Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
6 hours ago by Kai Xin • 0
1
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1
reply
168
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Retrieve a % coverage for each transcript
RNA-seq
updated 22 hours ago by 43k • written 22 hours ago by ▴ 40
0
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2
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260
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How can I solve this error?
metal
12 hours ago by 22211020193 • 0
0
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0
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102
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Struggling to lift genome builds
PLINK liftover GWAS
updated 22 hours ago by 141k • written 23 hours ago by • 0
1
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2
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199
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Can I readmap short reads to rDNA references?
rDNA assembly
updated 21 hours ago by 43k • written 23 hours ago by • 0
0
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0
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188
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Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
1 day ago by Ronin • 0
2
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6
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534
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Removing duplicates
duplicates ONT minimap2
7 hours ago by quentinperriere • 0
0
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1
reply
146
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Annotating a dataset with gnomAD v4 using Hail
Python Sequencing Hail Exome Annotation
updated 1 day ago by ▴ 40 • written 1 day ago by • 0
0
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1
reply
136
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Freyja plot error
Freyja
updated 1 day ago by 43k • written 1 day ago by • 0
0
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0
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101
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BIOM format can contain tabular data ?
BIOM phyloseq biomformat R
1 day ago by chemokine-1 ▴ 10
0
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4
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369
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How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
8 hours ago by feather-W • 0
0
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2
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168
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Bedmethyl file format
bedmethyl methylation
updated 1 day ago by 141k • written 1 day ago by ▴ 20
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0
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121
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sequence table for DADA2 chimera filtering
OTU sequencetable DADA2
1 day ago by Ali • 0
2
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4
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256
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SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by kirill.zaslavsky • 0
0
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2
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193
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Calculating percentage of cells proliferating in single cell rna seq data
statistics scRNA-seq proliferation
1 day ago by mropri ▴ 150
0
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1
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220
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How to get the reference panel for UKBB
UKBB GWAS clump
updated 22 hours ago by ★ 2.3k • written 1 day ago by • 0
0
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0
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117
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Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames RNA-Seq WGCNA unique
1 day ago by shasabhi1 • 0
0
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0
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109
views
How to summarize dbCAN3 results
dbCAN CAZy CAZyme dbCAN3 dbCAN2
1 day ago by Nishat • 0
0
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0
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118
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what exactly is a k-mer table (remora)?
remora basecall
1 day ago by anne • 0
1
vote
1
reply
150
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Help/Direction Needed for Data Analysis of RNA
Sequencing RNA-seq DNA-Seq
updated 1 day ago by ★ 5.8k • written 1 day ago by • 0
0
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0
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119
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GWAS Phenotypes
GWAS
2 days ago by solomoncharles77 ▴ 90
0
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2
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249
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GSEA analysis in R
GSEA R Arabidopsis
6 hours ago by Sudip • 0
0
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0
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102
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Add geno header to VariantAnnotation objects
nichenet scRNA-seq
2 days ago by QX • 0
2
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5
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325
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Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
1 day ago by Bikram Kumar • 0
0
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2
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219
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance Genomics RNA-seq Data-Analysis
updated 1 day ago by 43k • written 2 days ago by • 0
1
vote
2
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225
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Can I compare kallisto counts from samples with different amount of reads?
RNA-seq kallisto
1 day ago by bioinfo ▴ 150
0
votes
1
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166
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 2 days ago by ★ 2.3k • written 2 days ago by • 0
0
votes
1
reply
182
views
merging Seurat objects after SCT
Seurat SCT
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
1
reply
159
views
Two databases: Human Microbiome Project and MGnify
Microbiome databases
updated 2 days ago by 141k • written 2 days ago by ▴ 360
0
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2
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232
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RNAseq 1 control 2 different treatment
RNA-seq
2 days ago by matteo.levorato • 0
1
vote
0
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125
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Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology RNA-seq R
updated 2 days ago by 43k • written 2 days ago by ▴ 10
0
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0
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128
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by 141k • written 3 days ago by ▴ 150
2
votes
0
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181
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by Alexander ▴ 220
1
vote
1
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153
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 3 days ago by 141k • written 3 days ago by ▴ 80
0
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0
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116
views
Automated internal stop codon checker
ORF stopcodon internal virus
3 days ago by Balazs Horvath ▴ 10
0
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0
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117
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Repeat expansion identification tools for long-read data
fragilex repeatexpansion long-read fmr1
3 days ago by adarsh_pp ▴ 40
0
votes
0
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130
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FreeBayes detection capacity
reads freebayes long
3 days ago by quentinperriere • 0
144 results • Page 1 of 3
Recent Votes
Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
A: Extract fasta sequences from a file using a list in another file.
How to comparing two bacterial genomes and find the mutation, rearrangement etc.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: Korean reference file
How to get all genes for a specific list of regions in R preferably using Biomart
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Commentator to GenoMax 141k
Centurion to jkbonfield ★ 1.2k
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Recent Replies
Answer: Problem with Mirdeep2 and Randfold output by otieno43 ▴ 20
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file by GenoMax 141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle by Ram 43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle by Joseph • 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Answer: change gene IDs to gene name in RNAseq by Trivas ★ 1.7k
This has been answered a million times on this forum, see here https://www.biostars.org/p/430015/
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies by GenoMax 141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file by GenoMax 141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR by GenoMax 141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq by GenoMax 141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
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