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0 votes
1 reply
729 views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated by GenoMax GenoMax • written by ycts • ycts
1 vote
4 replies
3.3K views
DEG analysis of RNA-seq data across multiple tissues and two conditions
rna-seq edger degs deseq2
written by BioinfGuru BioinfGuru
1 vote
1 reply
1.1K views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf bam bcf snps
updated by LChart LChart • written by George • George
0 votes
4 replies
1.7K views
Per base sequence content failed miserably
fastqc sequence trimmomatic ngs assembly
written by Kai Xin • Kai Xin
0 votes
1 reply
651 views
Retrieve a % coverage for each transcript
rna-seq
updated by Ram Ram • written by jammydodger123456 • jammydodger123456
0 votes
2 replies
1.1K views
How can I solve this error?
metal
written by 22211020193 • 22211020193
0 votes
0 replies
556 views
Struggling to lift genome builds
plink liftover gwas
updated by GenoMax GenoMax • written by srimmer • srimmer
0 votes
4 replies
1.2K views
Can I readmap short reads to rDNA references?
rdna assembly
updated by GenoMax GenoMax • written by aniigodwinn • aniigodwinn
0 votes
3 replies
1.7K views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
written by valentinatsar • valentinatsar
0 votes
3 replies
1.7K views
Editing Human Reference Genome by adding a CDS
gff agat transcriptome
updated by Michael Dondrup Michael Dondrup • written by LDT • LDT
0 votes
11 replies
3.1K views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated by jkbonfield jkbonfield • written by me • me
0 votes
2 replies
1.5K views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edger
written by nhaus • nhaus
0 votes
0 replies
828 views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
homer atac-seq
written by Ronin • Ronin
0 votes
2 replies
4.5K views
How to convert SAM/BAM file to GTF/GFF file?
gtf sam bam gff minimap2
updated by Arslan Tariq • Arslan Tariq • written by BioinfoBee • BioinfoBee
0 votes
7 replies
3.4K views
Removing duplicates
duplicates ont minimap2
updated by noodle noodle • written by quentinperriere • quentinperriere
0 votes
1 reply
1.1K views
Annotating a dataset with gnomAD v4 using Hail
python sequencing hail exome annotation
updated by DKA • DKA • written by james.melhorn • james.melhorn
0 votes
4 replies
4.7K views
biomaRt error for different R version
biomart r
updated by GenoMax GenoMax • written by manaswwm manaswwm
0 votes
1 reply
673 views
Freyja plot error
freyja
updated by Ram Ram • written by Adyasha • Adyasha
1 vote
2 replies
936 views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis r microarray dexma combinedp
written by hagl • hagl
0 votes
0 replies
587 views
BIOM format can contain tabular data ?
biom phyloseq biomformat r
written by chemokine-1 • chemokine-1
0 votes
4 replies
2.4K views
How to reduce the variation of CIBERSORTx results?
cibersortx deconcolution
written by feather-W • feather-W
0 votes
0 replies
811 views
sequence table for DADA2 chimera filtering
otu sequencetable dada2
written by Ali • Ali
0 votes
4 replies
1.2K views
SnpEff annotates coding duplication as intronic?
snpeff
written by kirill.zaslavsky • kirill.zaslavsky
0 votes
4 replies
1.6K views
Calculating percentage of cells proliferating in single cell rna seq data
statistics scrna-seq proliferation
written by mropri mropri
1 vote
4 replies
4.2K views
genefu for PAM50 prediction
rna-seq breast cancer subtyping
updated by hamarillo • hamarillo • written by silviajserrano • silviajserrano
0 votes
10 replies
2.2K views
Piping samtools to R
r ngs bash samtools
written by noodle noodle
0 votes
2 replies
1.9K views
How to filter columns in a raw sparse matrix in R
matrix r
updated by bk11 • bk11 • written by bgbs • bgbs
0 votes
7 replies
1.9K views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
written by ntsopoul • ntsopoul
0 votes
2 replies
1.0K views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames rna-seq wgcna unique
updated by James • James • written by shasabhi1 • shasabhi1
0 votes
3 replies
1.3K views
trouble using sequenceTubeMap in chromium installed on WSL
vg
written by ayushm64 • ayushm64
0 votes
0 replies
745 views
what exactly is a k-mer table (remora)?
remora basecall
written by anne • anne
0 votes
6 replies
14K views
List of species in RepeatMasker Tool (species parameter)
repeatmasker masking
updated by Bioinfotec • Bioinfotec • written by nut_B • nut_B
0 votes
6 replies
2.5K views
Rename multiple fastq.gz files
fastq next-gen
updated by shenwei356 shenwei356 • written by Jérémie • Jérémie
0 votes
1 reply
706 views
Help/Direction Needed for Data Analysis of RNA
sequencing rna-seq dna-seq
updated by dsull dsull • written by niruf • niruf
0 votes
0 replies
963 views
Job: Ensembl Outreach Project Leader
ebi embl genomics ensembl
written by Ben Moore Ben Moore
0 votes
3 replies
1.4K views
Bwa sampe - BGI
bwa-sampe bgi
updated by GenoMax GenoMax • written by lorena9132 • lorena9132
0 votes
0 replies
1.0K views
News: Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop rna-seq nextflow dna-seq
updated by Ram Ram • written by David Langenberger David Langenberger
1 vote
3 replies
1.1K views
Forum: Bioinformatics: Where do I start
sequencing
updated by dromicslabs51 • dromicslabs51 • written by Adi • Adi
0 votes
2 replies
1.2K views
GSEA analysis in R
gsea r arabidopsis
written by Sudip • Sudip
1 vote
2 replies
2.2K views
Visualization of PROKKA Annotation Result?
prokka annotation
updated by Joe Joe • written by ferdinand • ferdinand
0 votes
2 replies
1.1K views
Which experiments generate Position Frequency Matrix?
position-frequency-matrix
written by Anisur Rahman • Anisur Rahman
0 votes
2 replies
1.4K views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Supplementary files from GEO?
geo velocity count-matrix
updated by Ram Ram • written by Spring • Spring
0 votes
0 replies
455 views
Add geno header to VariantAnnotation objects
nichenet scrna-seq
written by QX • QX
0 votes
4 replies
1.9K views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scrna-seq 10x
written by Spring • Spring
0 votes
5 replies
2.0K views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
written by Bikram Kumar • Bikram Kumar
0 votes
1 reply
1.4K views
WGCNA network from Adjacency or TOM matrix
wgcna network
updated by andres.firrincieli andres.firrincieli • written by Milly • Milly
0 votes
1 reply
715 views
Error in edgeR/Deseq2 Analysis
r edger
updated by ATpoint ATpoint • written by Ravita • Ravita
0 votes
2 replies
1.9K views
Getting marker genes for cell types
clustering marker-genes umap
written by orzrzlyo • orzrzlyo
0 votes
1 reply
1.1K views
gene body coverage with RSeqQC
rna-seq qc
updated by BioinfGuru BioinfGuru • written by wiscoyogi • wiscoyogi
0 votes
2 replies
928 views
Statistical Advice Needed for RNAseq Data Analysis
statistical-significance genomics rna-seq data-analysis
updated by Ram Ram • written by David • David
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