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0 votes
4 replies
1.9K views
TaxID mapping file
annotation blobtools rnaseq decontamination transcriptomes
updated by WaspInSpace 0 • | written by Lada 6
1 vote
0 replies
648 views
.lgen file has 3+ different alleles
plink lgen ped
updated by zx8754 1.2K • | written by Emilie 1
0 votes
0 replies
563 views
vcf procesing for ML antigen prediction
formats vcf fastaq hla_imputation hla_typing
written by Javier 0
0 votes
2 replies
1.3K views
Extracting mutation status from MAF files - TCGA
tcga maf mutation
updated by Zhenyu Zhang 130 • | written by yahn 1
0 votes
0 replies
608 views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic variant predisposition
written by mikemakaveli1 0
0 votes
2 replies
1.1K views
Raw counts using stringtie
stringtie rna-seq
updated by GenoMax 16K • | written by ahmad.sajad4541 0
0 votes
0 replies
702 views
Modify plot R mtDNA indel
plot mtdna r
written by marco.barr 22
0 votes
0 replies
1.0K views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot graphical_output gsea clusterprofiler
written by NorbertK 1
1 vote
2 replies
1.7K views
Analysis of intronic reads included scRNA-seq data
single-cell
updated by Ram 4.5K • | written by carolofharvest 6
3 votes
14 replies
5.5K views
High Malat-1 expression in single cell data
single-cell
updated by t.montserrat.ayuso 4 • | written by carolofharvest 6
0 votes
2 replies
884 views
Downloading older version of a tool
alignment tools
written by RT 0
0 votes
0 replies
795 views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization illumina ngs sequencing
written by rustykb 4
0 votes
1 reply
685 views
DSEQ2 analysis
deseq2 logfoldchange
updated by Ram 4.5K • | written by adi.gershon1 1
0 votes
5 replies
3.5K views
Generating mpileup file using samtools
mpileup samtools
updated by Joe 2.2K • | written by RT 0
1 vote
5 replies
8.8K views
What purposes can TPM values be used for?
rna-seq tpm normalization deseq2
updated by b.contreras.moreira 49 • | written by JH 1
0 votes
3 replies
1.2K views
Does comparing two different groups to a common third group introduce bias in the analysis?
deseq rnaseq
updated by ATpoint 9.1K • | written by Qi 0
0 votes
0 replies
953 views
News: Cellosaurus release 49 is available
cell biocuration line database news knowledgebase
written by Amos Bairoch 14
0 votes
3 replies
1.6K views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated by dthorbur 350 • | written by Vijith 10
0 votes
0 replies
652 views
SIngle cell analysis
seurat scrna-seq harmony doubletfinder merge
written by JY 0
0 votes
2 replies
1.8K views
homer not configured properly
homer maketagdirectory
updated by clairechung112 1 • | written by amahdi779 0
0 votes
3 replies
2.1K views
Bedtools merge minimum overlap?
bedtools genomics
updated by Alex Reynolds 3.6K • | written by SJP 0
0 votes
0 replies
821 views
Empty table plot using plotGseaTable()
fgsea
written by Chris 36
1 vote
1 reply
1.9K views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated by anovak 18 • | written by Hang 1
0 votes
3 replies
1.7K views
DiffBind: no peaks in DBA
macs2 diffbind chip-seq
updated by jared.andrews07 1.9K • | written by yvonneh 1
0 votes
5 replies
2.3K views
Converting CRAM to FastQ
gatk samtools cram samtofastq fastq
written by Maverick 1
1 vote
8 replies
9.2K views
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated by Sd 0 • | written by Nicolas Rosewick 1.1K
0 votes
2 replies
1.0K views
Base Quality Score Recalibration with different reference genome
snps gatk bqsr rna-seq
written by dtnondorf 0
0 votes
8 replies
2.3K views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16s amplicon dada2 ampliseq
updated by Chris Dean 42 • | written by sovrappensiero 10
0 votes
2 replies
1.2K views
RNA-seq data for deep learning classification
rna-seq
written by yahn 1
0 votes
8 replies
2.4K views
How to access TCGA samples that were treated with a specific drug?
tcga rna-seq
written by Qroid 4
0 votes
1 reply
2.1K views
Loss of 'var' using concatenation of AnnData objects
scanpy anndata
updated by Hugo 0 • | written by Rachel 0
0 votes
1 reply
703 views
Provean help
variant provean
updated by Mensur Dlakic 3.0K • | written by Arun Sai Kumar 0
0 votes
1 reply
1.6K views
Download eQTL data of one specific gene for all tissues from GTEx
eqtl gtex
updated by bk11 312 • | written by Jeol 2
0 votes
7 replies
2.0K views
How does gene length effect the number of reads mapped
rna-seq cpm sequencing
written by Chen 0
0 votes
5 replies
1.8K views
Problem with data downloaded from Short Reads Archive (SRA)
sra dada2 metabarcoding
updated by atharvakarkare14 4 • | written by Begonia_pavonina 22
0 votes
8 replies
3.1K views
Downsampling long-read BAM files
nanopore bam qc ont downsampling
written by eebloom 11
0 votes
3 replies
1.2K views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
gene-expression rna noiseq dge
updated by ATpoint 9.1K • | written by alifafiq1 0
0 votes
0 replies
418 views
Use of annotation of integrated Seurat object in single sample
seurat
written by Nona 9
0 votes
0 replies
558 views
News: Beyond beginner R: Advancing your coding skills - September 16-19
advanced-coding programming r
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
1 reply
940 views
Subsetting and merging back Seurat Object brings different results
seurat
written by Nona 9
0 votes
0 replies
962 views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
ngs genomics post-doc r-loops
updated by Ram 4.5K • | written by 4r-rtg 0
1 vote
1 reply
761 views
Discrepancy in read counts from fastq
downsampling fastq
updated by Ram 4.5K • | written by marco.barr 22
0 votes
0 replies
684 views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
written by Vijith 10
0 votes
14 replies
4.3K views
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated by GenoMax 16K • | written by nicole.kavanagh 0
0 votes
1 reply
1.4K views
Is there a way to increase the automatic label text size in Cytoscape?
cytoscape
updated by Scooter 31 • | written by avocado123 0
0 votes
0 replies
825 views
Combining Methylation Microarray data from different platforms
microarray dna epic 450k methylation
written by James 3
0 votes
1 reply
1.3K views
Basic stats in hierfstat
fst stats hierfstat
updated by mdav 0 • | written by Zoe 0
0 votes
3 replies
1.2K views
Odd alignment question/finding
alignment
updated by barslmn 245 • | written by poordumbsillyidiot 0
0 votes
1 reply
767 views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
gatk recalibration
updated by GenoMax 16K • | written by mgranada3 6
0 votes
0 replies
554 views
Looking for the best way to interpret these data
rna-seq ontology go
updated by Ram 4.5K • | written by Oscar 1
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