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0 votes
3 replies
1.1K views
cutadapt not working when calling in a bash code with qsub
qsub trim cutadpat
updated by ATpoint 9.1K • | written by Meghan.T 1
0 votes
3 replies
1.8K views
Removing features from RNA assay in seurat
r seurat sc-rna-seq
updated by yura.grabovska 94 • | written by Varun Gupta 129
0 votes
0 replies
766 views
News: Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November)
genome-assembly pacbio long-reads hi-c
written by Physalia-courses 281
0 votes
6 replies
2.0K views
miRNAseq - over-presented sequence in negative control
mirnaseq adaptor dimer
updated by Ant 5 • | written by MH85 2
0 votes
0 replies
526 views
Differential expression analysis from .chp files with Limma
expression limma iontorrent differential
written by Rogerio Ribeiro 11
0 votes
2 replies
1.7K views
Genome Polishing nextPolish
nextpolish2 nextpolish pilon racon
written by SomeOne 33
0 votes
1 reply
783 views
co-occurrence matrix from my VCF file
co-occurrence vcf
updated by robben 0 • | written by HarperReed 1
0 votes
6 replies
3.4K views
Center multiple pheatmap
pheatmap patchwork
updated by yura.grabovska 94 • | written by 5utr 37
0 votes
3 replies
1.3K views
creat histogram in R
r ggplot2 hist
updated by ATpoint 9.1K • | written by G.S 6
0 votes
5 replies
2.2K views
constructing gene-based pangenome from orthofinder output file
orthofinder pan-genome
updated by Dunois 301 • | written by Bushra Bibi 8
0 votes
6 replies
1.9K views
Genome Assembly Sorting
genome assembly sorting
updated by GenoMax 16K • | written by SomeOne 33
0 votes
3 replies
1.6K views
Install PacBio lima via conda fails
conda
updated by colindaven 844 • | written by michael.flower.14 21
0 votes
3 replies
1.1K views
human_variation_vcf
baserecalibrator
written by runfreely2 0
0 votes
2 replies
883 views
How to interpret Eigengene dendrongram results
eigengene dendrogram
written by nuorain 4
0 votes
24 replies
6.8K views
GTF file
cellranger-arc gtf cellranger-arc-2.0.2
written by IrK 10
1 vote
6 replies
1.6K views
Explanation of DESeq factor leveling
deseq
written by bthom 1
0 votes
1 reply
683 views
Allele frequency plot : imputed vs reference panel variants
imputation genotyping reference
updated by BlastedBadger 16 • | written by hello_genome 0
0 votes
1 reply
649 views
rRNA contamination after filtering
qc contamination ribosomal-rna
updated by GenoMax 16K • | written by sleepystudent 0
1 vote
0 replies
601 views
Repeated ensembl IDs in microarray DEG analysis
r annotation degs microarray limma
written by Pereira G 1
0 votes
2 replies
1.2K views
How to filter annotated genes overlapping with TE/repeat element?
genome gene annotation
written by Yao 3
6 votes
13 replies
3.8K views
Forum: How to do datamining in bioinformatics
data-mining
updated by LauferVA 497 • | written by Biomed-jeh 8
1 vote
3 replies
3.2K views
Why parametric linkage analysis on Merlin gives zero "0" LOD score?
snp alohomora merlin
updated by Ram 4.5K • | written by eDNAuRNA 2
0 votes
2 replies
1.8K views
Single-cell RNA differential expression with an unbalanced number of cells between conditions
single-cell differential-expression
written by Javi.villegas21 0
0 votes
1 reply
753 views
What are the epithelial cells subtype in esophagus tissue ?
python scanpy anndata single-cell
updated by ATpoint 9.1K • | written by AlexStar 22
0 votes
0 replies
683 views
News: ONLINE COURSE – Genome Assembly and Annotation (GAAA01)
annotation genome assembly genomics
updated by GenoMax 16K • | written by oliverhooker 14
0 votes
1 reply
816 views
News: Course: Single-cell RNA-seq analysis with R/Bioconductor
bioconductor single-cell-rnaseq
updated by yura.grabovska 94 • | written by Physalia-courses 281
0 votes
0 replies
733 views
Query regarding interpretation of VCF from variant calling (SVs) using vg giraffe workflow
pangenome giraffe vcf vg
written by s_135 1
1 vote
2 replies
2.0K views
Query about vg (and vg giraffe) for pangenome creation and VC
pangenome giraffe vg
written by s_135 1
0 votes
4 replies
2.0K views
GSVA with a genelist on a "per-cluster" basis
gsva scrna-seq genelist
written by bio_info 2
0 votes
0 replies
393 views
Checking Sequence Duplication or errors in a de novo transcriptome assembly
duplicatedsequences assemblyerror redundantsequences denovotranscriptome
written by ZuelTech 0
0 votes
0 replies
477 views
Pausin index for qpro-seq
pausing qpro-seq index
written by daffodil 1
0 votes
2 replies
1.2K views
Selecting appropriate expressed repeat annotation for Velocyto
velocyto repeatmasker scrnaseq
written by merdanosman 0
0 votes
1 reply
752 views
Regions got skipped due to length
getfasta bedtools
updated by Pierre Lindenbaum 17K • | written by Muhammad 0
0 votes
10 replies
2.0K views
Using a different reference transcriptome assembly from different RNA seq libraries (but same species)
transcriptomeassembly libraries
written by ZuelTech 0
0 votes
3 replies
1.6K views
Error function vst in DESeq2
vst deseq2
updated by yura.grabovska 94 • | written by Larissa 0
0 votes
3 replies
1.2K views
Tumor purity in TCGA data analysis
tcga tumor-purity
updated by Ram 4.5K • | written by nuorain 4
0 votes
0 replies
742 views
Help with EIGENSOFT's SmartPCA
smartpca eigensoft pca
written by Persona 0
0 votes
0 replies
551 views
Matching of GSVA score of a single sample to its drug sensitivity
gsva
written by marionette.kent 0
0 votes
1 reply
1.2K views
Software For MHC Typing Using Mouse NGS (WES or RNAseq)?
mhc
updated by mourisl 3 • | written by kilcdincer 1
0 votes
1 reply
1.4K views
DMRCate mean diff values
design methylation dmrcate
updated by james.hawley 10 • | written by Eren 0
0 votes
1 reply
569 views
Looking for any study/research paper that used gcPathogen database
gcpathogen
updated by GenoMax 16K • | written by Albert 0
0 votes
2 replies
1.4K views
Convert two Haplotypes into diploid genome assembly
goneme assembly
written by Yiyi 0
0 votes
1 reply
908 views
Performance Issues with GATK4 PathSeqPipelineSpark on 35bp Bulk-RNA Unmapped Reads
pathseq
updated by colindaven 844 • | written by xutongzhen1996 0
0 votes
12 replies
4.0K views
GATK3 error message
gatk next-gen
updated by Ram 4.5K • | written by shuksi1984 6
1 vote
8 replies
3.1K views
ATAC-seq peaks centered between TSS and TES
compute-matrix atac atac-seq tss-enrichment enrichment-graph
written by buffealo 13
0 votes
3 replies
1.2K views
Identifying true variants between two strains despite low coverage
vcf bcftools mpileup variant-calling
updated by GenoMax 16K • | written by bioinfo1994 2
0 votes
0 replies
984 views
Are there "gold standard" datasets for identification of antibiotic resistance genes from metagenomic samples?
amr antibiotic resistance classification metagenomics
written by Bertalan_Takacs 14
0 votes
7 replies
1.8K views
how to find the number of exome bases covered in bam file
bam coverage
updated by GenoMax 16K • | written by Smilesky 0
0 votes
3 replies
1.2K views
lacking reference transcriptome
transcriptome enrichment
updated by ATpoint 9.1K • | written by Sarah 0
0 votes
0 replies
638 views
News: Introduction to CRISPR-Cas9 course
genome-editing crispr evolution
updated by Ram 4.5K • | written by Physalia-courses 281
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