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0 votes
1 reply
774 views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation vcf vep zygosity deepvariant
written by asalimih • asalimih
0 votes
0 replies
537 views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity metatranscriptome
written by jway • jway
0 votes
2 replies
1.8K views
Cannot install bwa-mem2 via conda
conda mamba python
updated by Ram Ram • written by jsmith120f • jsmith120f
0 votes
3 replies
1.5K views
genome finishing
finishing genome
updated by sihan.bu • sihan.bu • written by trezini • trezini
0 votes
5 replies
2.1K views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos atacseq
updated by Pierre Lindenbaum Pierre Lindenbaum • written by biology_inform • biology_inform
0 votes
4 replies
1.4K views
Add stats to boxplot in R
stats r
written by G.S • G.S
0 votes
1 reply
3.6K views
Seurat v5 and how to correctly integrate across multiple experiments
seurat scrna r
updated by Papyrus Papyrus • written by yura.grabovska • yura.grabovska
0 votes
1 reply
1.7K views
Difference in number of reads when using duplex and simplex base calling with Dorado
base calling nanopore simplex dorado duplex
updated by GenoMax GenoMax • written by Lélé • Lélé
0 votes
5 replies
1.7K views
calculating genomic coverage/ base overlap in R
genomics
updated by 1769mkc 1769mkc • written by Xbox_27 • Xbox_27
0 votes
5 replies
2.1K views
Annotating file using bcftools
annotation plink bcftools
written by kl • kl
0 votes
9 replies
4.5K views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
written by njornet • njornet
0 votes
3 replies
1.2K views
Problem with Calling Variants from RNA-Seq data
vcf gatk benchmark giab rna-seq
written by Esraa • Esraa
0 votes
4 replies
2.1K views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
manorm chip-seq consensus peaks
written by Alexandra • Alexandra
3 votes
1 reply
1.4K views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated by dariober dariober • written by Holly • Holly
0 votes
0 replies
376 views
ReactomeGSA
reactomegsa
written by Shaimaa Gamal • Shaimaa Gamal
0 votes
0 replies
469 views
News: New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
keeplearning tscourses
written by Transmitting Science communication • Transmitting Science communication
0 votes
5 replies
1.7K views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated by GenoMax GenoMax • written by chrisk • chrisk
0 votes
1 reply
1.1K views
perseus software (version 1.5.5)
mass spectrometry preseus data
written by Bioinformatics_16 • Bioinformatics_16
0 votes
0 replies
609 views
Why the shape of RCS is contradictory to the p value for nonlinearity.
rcs ggplot2 ggplot r
updated by GenoMax GenoMax • written by Dude • Dude
0 votes
0 replies
511 views
NEURON, Brian2, NEST, or PyNN
nest neuron pynn brian2
written by brunofelicianodeomena • brunofelicianodeomena
0 votes
2 replies
6.2K views
Alphafold 3 pLDDT coloring scheme in chimerax?
chimerax alphaphold alphaphold3
updated by colindaven colindaven • written by mbrav005 • mbrav005
0 votes
1 reply
803 views
Polish a large genome with Pilon
pilon pacbio polish illumina
written by san96 • san96
0 votes
2 replies
997 views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation transposableelements
written by MarcosCosta • MarcosCosta
1 vote
2 replies
1.2K views
Genome Visualization Tools
bacterial genome
updated by GenoMax GenoMax • written by dlera.lozano • dlera.lozano
0 votes
3 replies
1.4K views
RSeQC : infer_experiment.py Error: Could not retrieve index file
rseqc rna-seq
updated by Ram Ram • written by Prawesh • Prawesh
0 votes
3 replies
1.3K views
Using ggplotly in R
ggplot ggplotly
updated by jared.andrews07 jared.andrews07 • written by jen • jen
0 votes
3 replies
1.4K views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart rnaseq kallisto
written by bioinfo • bioinfo
0 votes
3 replies
1.4K views
RNAseq RNA content
mrna linux rrna rna-seq rna
updated by noodle noodle • written by doramora • doramora
0 votes
1 reply
1.1K views
Post-imputation QC for input into GWAS analyses
gwas prs
updated by LauferVA LauferVA • written by graeme.thorn graeme.thorn
0 votes
2 replies
2.0K views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming adapters cutadapt srna-seq smallrna
written by melissa.joubert • melissa.joubert
2 votes
1 reply
1.9K views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
written by J. • J.
0 votes
0 replies
506 views
Is there a real ground truth for CNV data?
cnv
written by jennyp0706 • jennyp0706
0 votes
3 replies
1.2K views
Biomart issue, why so few 3'utrs?
utr biomart
updated by GenoMax GenoMax • written by RNAseqer RNAseqer
0 votes
1 reply
556 views
sci-RNA-seq
seurat sci-rna-seq
updated by Ram Ram • written by kilcdincer • kilcdincer
0 votes
4 replies
4.8K views
CNVkit for somatic copy number detection
cnv cnvkit exome wes
updated by Anitha • Anitha • written by stephaniem • stephaniem
0 votes
8 replies
3.2K views
Overlapping Ranges within Granges object
genomicranges iranges granges
updated by Alex Reynolds Alex Reynolds • written by ntsopoul • ntsopoul
0 votes
3 replies
847 views
How to access GWAVA software of data
gwava
updated by GenoMax GenoMax • written by nonaddldy • nonaddldy
0 votes
2 replies
1.0K views
Inquiry about deseq2 transformation
rna-seq deseq2
written by Chen • Chen
0 votes
1 reply
774 views
The total expressed genes in RNA-Seq data
rna-seq
updated by ATpoint ATpoint • written by Pegasus • Pegasus
0 votes
1 reply
900 views
What is the bin size for Bamcompare?
chip-seq deeptools bamcompare
updated by Ram Ram • written by Emily • Emily
0 votes
3 replies
2.0K views
Is there any way to modify this pie chart ?
pie ggplot r chart
updated by GenoMax GenoMax • written by ohtang7 • ohtang7
0 votes
0 replies
598 views
In what situations is 'outer' typically used when using anndata.concat()?
concat anndata scanpy
written by Spring • Spring
1 vote
3 replies
1.5K views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp filteration genotype quality gatk
updated by mufernando • mufernando • written by IdaHao0921 • IdaHao0921
0 votes
3 replies
1.5K views
Snakemake wrapper issue
fastqc snakemake
updated by Wei-Chen Pan • Wei-Chen Pan • written by Matvii Mykhailichenko • Matvii Mykhailichenko
0 votes
5 replies
2.7K views
What does the 'E%' represent in BUSCO results?
busco
updated by Philipp Bayer Philipp Bayer • written by 林明德 • 林明德
0 votes
4 replies
5.4K views
MGLTools does not work in windows 11
windows-11 autodock windows mgltools
updated by Ram Ram • written by mohyeddine.taleb • mohyeddine.taleb
0 votes
4 replies
2.1K views
Help with IGV abbreviation
igv
updated by Ram Ram • written by GeneC • GeneC
0 votes
1 reply
767 views
How to process Bulk WES data?
wes wgs
updated by GenoMax GenoMax • written by wyuan37 • wyuan37
1 vote
1 reply
1.1K views
Can diamond prepdb be used to make a taxonomically aware database?
blast diamond taxonomy
updated by GenoMax GenoMax • written by cedric.blais • cedric.blais
0 votes
2 replies
1.6K views
News: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
dna-seq variant-calling rna-seq illumina transcriptomics
written by David Langenberger David Langenberger
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