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0 votes
0 replies
612 views
Beagle 4.1 cannot remove batch effect caused by NGS read depth
beagle batch-effect sequencing-depth
updated by Ram Ram • written by Qi • Qi
284 votes
33 replies
142K views
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated by tshtatland tshtatland • written by Obi Griffith Obi Griffith
0 votes
2 replies
1.6K views
Confusion Regarding Tape Station Peak
library transcriptome
updated by colindaven colindaven • written by Bhavya • Bhavya
0 votes
6 replies
1.8K views
GATK4 haplotypecaller calls variants on regions without read coverage
gatk4 cnnscorevariants haplotypecaller
written by thomas.heigl.ibk • thomas.heigl.ibk
0 votes
7 replies
2.2K views
Hard to automatically download NCBI protein IDs
ncbi batch-download
updated by Ram Ram • written by The The
0 votes
0 replies
632 views
VG: Get input file error
vg
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Taek • Taek
1 vote
2 replies
1.4K views
Somatic Variant Calling from Nanopore Data
variant somatic calling cancer nanopore
updated by GenoMax GenoMax • written by adarsh • adarsh
0 votes
9 replies
5.4K views
Running vcf2maf on snpeff-annotated vcfs
vcf2maf snpeff
updated by Ram Ram • written by becky3.a • becky3.a
0 votes
0 replies
868 views
the number of reads pre and post running "isoseq refine"
isoseq pacbio
written by wqqgenetics • wqqgenetics
0 votes
6 replies
2.0K views
Why Can’t I Find the URL and Details for I-Mutant3.0? Does It Even Exist? Urgent Help Needed from Experts!”
i-mutant
written by 半桶 • 半桶
0 votes
2 replies
1.3K views
Job: Freelancer - to set up a server running space ranger?
linux-server space-ranger
updated by Michael Dondrup Michael Dondrup • written by ia2240 • ia2240
0 votes
4 replies
1.7K views
No mouseOver effect in my track hub on UCSC genome browser
ucsc-genome-browser
updated by Ram Ram • written by Pei Pei
0 votes
1 reply
1.1K views
Quality check in long read (ONT, PacBio) bam files
qc bam minimap2
updated by GenoMax GenoMax • written by shinyjj • shinyjj
0 votes
1 reply
841 views
tag definations in GAF file produced by vg giraffe
vg
written by chuanj8848 • chuanj8848
1 vote
0 replies
853 views
How to generate a GAF that shows alignments to all component genomes in graph
pangenome minigraph vg minigraph-cactus
written by peterdfields • peterdfields
0 votes
4 replies
3.0K views
Fragmented BUSCOs of genome assemblies - How to improve scores?
fragmented buscos
updated by young_bioinformatician young_bioinformatician • written by neolycus • neolycus
0 votes
0 replies
669 views
Branches are too far from the leaves in the circular tree display with ete3
ete3 circular-tree
updated by Ram Ram • written by Bertrand • Bertrand
0 votes
4 replies
1.9K views
How to assign cell types after integration in scRNA
scrna-seq
updated by OmnibusX • OmnibusX • written by Francesco • Francesco
3 votes
0 replies
665 views
News: Registration for the Nextflow Summit is still open. Get a 20% discount!
seqera nextflow
updated by Ram Ram • written by Marcel Ribeiro-Dantas • Marcel Ribeiro-Dantas
0 votes
4 replies
1.7K views
AWK for replacing the content of a column in a csv file with the content of another column from another csv WITHOUT USING THE COLUMN NUMBER
bash awk csv
updated by GenoMax GenoMax • written by giulia.trauzzi • giulia.trauzzi
0 votes
2 replies
1.1K views
Where do I gather indel and frameshift information in SnpEff output?
frameshift wgwps snpeff gatk indels
written by mgranada3 • mgranada3
4 votes
1 reply
1.1K views
Cannot use more than 2 sample IDs when demultiplexing using Demuxlet
snp variant demultiplexing demuxlet scrnaseq
written by Chilly • Chilly
0 votes
0 replies
680 views
News: EMBO Practical Course Measuring translational dynamics by ribosome profiling
emboriboprof
written by EMBL Events EMBL Events
0 votes
0 replies
801 views
News: EMBL Conference The expanding world of RBPs: from posttranscriptional control to riboregulation
emblrbp
written by EMBL Events EMBL Events
1 vote
0 replies
711 views
News: EMBL Course Computing skills for reproducible research: software carpentry
emblsoftwarecarpentry
updated by Jean-Karim Heriche Jean-Karim Heriche • written by EMBL Events EMBL Events
0 votes
0 replies
694 views
News: Course: Project Structure for Reproducible Work
workflows programming reproducibility replicability
updated by Ram Ram • written by filip.buric • filip.buric
0 votes
6 replies
2.5K views
normalization in single cell
normalization scrna-seq single-cell
updated by Bastien Hervé Bastien Hervé • written by kayah • kayah
0 votes
1 reply
996 views
How to Visualize ATAC-seq Peaks with Transcription Factor Binding Sites Using IGV
tf igv atacseq
updated by Bastien Hervé Bastien Hervé • written by giegie • giegie
0 votes
0 replies
730 views
News: Coding Courses @ Edinburgh Genomics
snakemake python r workshop linux
written by Kat @ EdGe • Kat @ EdGe
0 votes
0 replies
555 views
Digital Pathology feature pooling methods
feature-pooling ai
updated by Ram Ram • written by Eren • Eren
0 votes
3 replies
1.4K views
How to download NCBI's Identical Protein Group (IPG) database
efetch ipg entrez ncbi
updated by Irsan Irsan • written by Peter • Peter
1 vote
2 replies
2.3K views
pathview - cannot open URL : HTTP status was '403 Forbidden'
r kegg pathview
updated by lianchee11 • lianchee11 • written by Itamar • Itamar
0 votes
1 reply
899 views
Sorting DEGs in the dotplot for every column
scrnaseq
updated by Bastien Hervé Bastien Hervé • written by ashkan ashkan
1 vote
1 reply
1.4K views
How can I convert a .sqn file to .gbk
genbank
updated by michael.ante michael.ante • written by madders73 • madders73
0 votes
3 replies
1.3K views
Unable to remove duplicate sequences
duplicate sequences removing
updated by michael.ante michael.ante • written by juanluis0516 • juanluis0516
0 votes
3 replies
1.5K views
remove duplicates in Nanopore cDNA PCR data
nanopore picard minimap2 duplicates pcr
updated by jeevii • jeevii • written by 静 • 静
0 votes
3 replies
1.5K views
ST: clustering on each tissue section separately or clustering on all tissue sections combined in Anndata object
spatial-transcriptomics squidpy scanpy
updated by OmnibusX • OmnibusX • written by Genomancer • Genomancer
0 votes
2 replies
1.5K views
Only two fastqs for 10X scATAC-seq data deposited on GEO database.
scatac-seq cellranger single-cell 10x
written by 1048686151 • 1048686151
0 votes
3 replies
2.4K views
IGV and display of amino acid translations
igv amino-acids
updated by Ram Ram • written by sk • sk
0 votes
0 replies
465 views
Using Arriba on single cell data set (scRNA-seq)
scrna-seq
written by sogand • sogand
0 votes
2 replies
1.3K views
Obtaining clinical data from the TCGA data portal
cancer hg38 tcga
written by elisheva elisheva
0 votes
0 replies
525 views
Encoding protein sequences based on catalytic residues
of functional proteins annotation
updated by GenoMax GenoMax • written by Nilavrah • Nilavrah
1 vote
6 replies
1.9K views
Download files from Experiment Acession
bioproject ncbi sra
written by Manuel Sokolov Ravasqueira • Manuel Sokolov Ravasqueira
0 votes
0 replies
725 views
Generate the snpfile.txt (for BLUPF90 input) in 0125 format from plink flat file (.map and .ped)?
genotype blupf90 plink
updated by GenoMax GenoMax • written by tvibhaps • tvibhaps
0 votes
6 replies
2.5K views
Associate Roary output with locus_tag from specific genome
bacteria locus_tags genomics
updated by Joe Joe • written by jennahamlin • jennahamlin
0 votes
5 replies
1.8K views
Segmentation fault PLINK 1.90b
plink
updated by chrchang523 chrchang523 • written by Alexandros.Frydas • Alexandros.Frydas
0 votes
6 replies
3.6K views
ROSE called super-enhancers overlapping with promoters
super-enhancers rose chip-seq
updated by jared.andrews07 jared.andrews07 • written by os306 • os306
0 votes
0 replies
1.1K views
Job: Bioinformatics Analyst - Laboratory Medicine and Pathology
job
written by toddknutson toddknutson
0 votes
2 replies
1.3K views
Hard filtering to reduce false positive variants due to poly track sequences
gatk
updated by GenoMax GenoMax • written by ManuelDB ManuelDB
0 votes
1 reply
1.1K views
A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
gatk vcf qd variantrecalibrator
updated by raphael.B • raphael.B • written by sam_brown_araujo • sam_brown_araujo
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