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0 votes
3 replies
1.5K views
Attempting to generate a sam file that can be converted to a bam file using samtools.
minimap2 samtools
updated by GenoMax 16K • | written by dlera.lozano 1
1 vote
9 replies
2.3K views
Using VEP annotation output as the input for a second VEP annotation
annotation vep vcf
written by Arton 2
0 votes
0 replies
868 views
Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
qc blacklist chip-seq
written by kalavattam 85
0 votes
1 reply
1.3K views
Optimal MACS2/3 configuration for paired-end ChIP-seq data: `-f BAM` versus `-f BAMPE`
macs3 peak-calling macs2 chip-seq
updated by ATpoint 9.1K • | written by kalavattam 85
1 vote
21 replies
3.7K views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
written by Bushra Bibi 8
1 vote
0 replies
824 views
News: Cellosaurus release 48 is available
cell-line biocuration cellosaurus knowledgebase
written by Amos Bairoch 14
0 votes
1 reply
1.0K views
Obtain rsID GWAS variants (9M)
dbsnp gwas rsid
updated by Ram 4.5K • | written by spolo 0
0 votes
1 reply
682 views
NCBI entrez-direct C++ Exception EUTILSAPP(CException::eInvalid)
ncbi
updated by GenoMax 16K • | written by Abdullah 0
0 votes
2 replies
1.1K views
Can I choose the sanger sequencing?
mutation sanger-sequencing
updated by Joe 2.2K • | written by Sabine 7
0 votes
0 replies
568 views
Human vs Mouse - Homologues
rnaseq homology
written by andrebolerbarros 0
0 votes
1 reply
1.1K views
DESeq2 and Gene Set Enrichment Analysis
deseq gsea
updated by ATpoint 9.1K • | written by noerm123 0
1 vote
2 replies
3.4K views
Methods to analyze EM-seq data
methylation wgbs em-seq
updated by Ram 4.5K • | written by Lluís R. 124
0 votes
1 reply
665 views
How to Annotating Human Genomic Variants for Disease Associations?
r variant-annotation gwas
updated by Ram 4.5K • | written by octpus616 14
0 votes
8 replies
2.4K views
Blastn for all bacteria genomes; create the db
blast blastn
updated by GenoMax 16K • | written by davidmaimoun 6
0 votes
0 replies
678 views
News: Online course: Genome Assembly Using Oxford Nanopore Sequencing
genome-assembly nanopore
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
0 replies
741 views
Tools for network alignement
graph network r netcom igraph
updated by Ram 4.5K • | written by Arindam Ghosh 55
0 votes
8 replies
3.3K views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE algorithm. Any suggestion
super-enhancers enhancers
updated by jared.andrews07 1.9K • | written by Manhezz 0
0 votes
2 replies
1.1K views
Suitable tool for mapping NGS data from enrichment experiment on combinatorial library
salmon ngs bwa combinatorial-library
written by Filip 0
0 votes
1 reply
690 views
combined bam files
rna-seq bam
updated by biofalconch 132 • | written by adi.gershon1 1
0 votes
0 replies
1.1K views
How to dock compounds with Si to a protein using Autodock vina?
docking ligands molecular
updated by GenoMax 16K • | written by Akhilesh 0
0 votes
1 reply
716 views
EnhancedVolcanop plot using GSE data
microarray gse enhancedvolcano
updated by bk11 312 • | written by mnx0723 0
0 votes
0 replies
615 views
"Conformer generation is disallowed since too many atoms" or "too flexible" in PubChem 3D conformer. Can I perform docking with such compounds?
docking ligands
updated by GenoMax 16K • | written by Akhilesh 0
0 votes
0 replies
726 views
Monocle3 cell data set object (grabbing values from one column)
scrna-seq monocle3 celldataset
updated by Ram 4.5K • | written by seattlescientist_01 0
0 votes
0 replies
402 views
Design microsatellite primers
microsatellite-primer molecular-identification
updated by Ram 4.5K • | written by sanjana.f 0
0 votes
1 reply
725 views
Which level does protein bioinformatics work at?
protein
updated by Michael Dondrup 5.6K • | written by 4fzcgueyp5 0
1 vote
2 replies
1.4K views
Why do these two variants appear to result in the same amino acid change when annotated by snpeff, but are annotated differently in clinvar
clinvar
written by curious 90
0 votes
0 replies
792 views
Job: Job Vacancy Announcement - Health Scientist Administrator (Program Officer) - Translational Genomics for Mental Health (TGMH)
program-officer translational-genomics
updated by Ram 4.5K • | written by NIMH Search 0
0 votes
0 replies
608 views
Forum: tutorial for carrier screening analyses?
carrier-screening
updated by Ram 4.5K • | written by Akos 2
1 vote
1 reply
1.0K views
Get VCF-format positions from coding positions
ngs dna vcf
updated by Ram 4.5K • | written by captainlabman 2
0 votes
1 reply
695 views
Visualize module preservation results
module-preservation wgcna
updated by Ram 4.5K • | written by Gail 0
0 votes
0 replies
573 views
Does anyone know of more tools like Enhancer Atlas?
transcription-factor enhanceratlas
updated by Ram 4.5K • | written by Rajashree 0
1 vote
2 replies
2.3K views
msa to use in alphafold
alphafold msa
updated by dthorbur 350 • | written by andreapamela.aguilar 1
0 votes
1 reply
2.1K views
Data scaling in single-cell RNAseq - sample-wise or on the full set?
scrna-seq seurat
updated by bk11 312 • | written by e.r.zakiev 26
0 votes
3 replies
1.5K views
Get the gene functions specific for clusters (RNA seq)
rnaseq heatmap clustering
updated by jv 187 • | written by Diana 1
1 vote
2 replies
2.0K views
Scaffolding contigs assembled with hifi reads
genome scaffolding hifi
written by stjerne 1
0 votes
1 reply
814 views
breed purity test analysis
breed-purity
updated by Ram 4.5K • | written by m90 3
0 votes
2 replies
1.0K views
How can I view the information in an alternative allele?
vcftools bcftools vcf annovar
updated by Ram 4.5K • | written by iarmir 1
1 vote
3 replies
1.5K views
Conditional coloring of heatmap
genomics heatmap complexheatmap single-cell
updated by Ram 4.5K • | written by ilomilo 1
0 votes
3 replies
991 views
GCP Snakemake
snakemake gcp
updated by GenoMax 16K • | written by Fadwa 1
0 votes
1 reply
839 views
cellranger process could not be killed
cellranger linux single-cell
updated by Ram 4.5K • | written by keke 0
0 votes
1 reply
1.2K views
GATK's CNV-caller output, genotype code?
gatk cnv ngs
updated by Rui Xu 0 • | written by Joel Wallenius 22
1 vote
5 replies
15K views
Relatedness vs relatedness2 from vcftools give different results
relatedness kinship
updated by mirkocelii 0 • | written by Sharon 61
0 votes
0 replies
465 views
Correlating Chip-Seq and proteimics results
chip-seq correlations proteomics
written by Assa Yeroslaviz 197
0 votes
1 reply
808 views
BLASTx Number of Matches
blastx blast
updated by Philipp Bayer 888 • | written by suyuqi 0
1 vote
7 replies
2.7K views
Increased proportion of heterozygous SNPs when RNAseq reads are mapped against a transcriptome
transcriptome snp rna-seq
updated by Ram 4.5K • | written by thal 1
0 votes
7 replies
1.9K views
What tools exist for filtering hundreds of VCFs (and annotated into VCFs in txt format) with GUI?
varaft vcf-miner filtering annotation
updated by Jeremy Leipzig 2.3K • | written by iarmir 1
0 votes
1 reply
730 views
Differential Expression using Scanpy
single-cell
written by Skamboj 0
0 votes
4 replies
2.4K views
Differing p-value cutoffs of limma derived DEGs in volcanoplots
timecourse rnaseq limma deg
written by JirMan 5
0 votes
2 replies
822 views
Correcting Farm effects
farm-effect
updated by Ram 4.5K • | written by Jeyamalar 0
0 votes
2 replies
1.1K views
I ran STAR, but essential output files did not generate.
star
updated by Ram 4.5K • | written by ZZOYEA 2
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