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0 votes
2 replies
1.3K views
extracting reads from FASTA/FASTQ file
rna-seq rna
updated by GenoMax GenoMax • written by bleven • bleven
0 votes
0 replies
34 views
Forum: biotech
biotech
updated by Arup Ghosh Arup Ghosh • written by Dara • Dara
0 votes
0 replies
1.2K views
Forum: epitope-TCR binding prediction, vaccine design
vaccine epitope-tcr binding
written by Dara • Dara
1 vote
1 reply
1.1K views
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
bulkrnaseq lme4
updated by ATpoint ATpoint • written by bioyas • bioyas
0 votes
1 reply
1.1K views
DeSeq2 filter transcripts
deseq2 rna-seq rna
updated by seidel seidel • written by bleven • bleven
0 votes
0 replies
542 views
Setting up a case control with 18 VCFs in plink?
case-control plink wgs
written by atopasn1 • atopasn1
0 votes
1 reply
909 views
Aligning to transcriptome with STAR generates error in Salmon sequence length
star salmon rnaseq
updated by Dunois • Dunois • written by Lena • Lena
0 votes
1 reply
829 views
Gnomad result tables column meaning.
gnomad annotation
updated by Pierre Lindenbaum Pierre Lindenbaum • written by ijarne • ijarne
1 vote
4 replies
1.9K views
DESeq2: adjusted p-values become NA when sub-setting samples
r deg rna-seq deseq2
updated by GenoMax GenoMax • written by txema.heredia • txema.heredia
0 votes
2 replies
1.6K views
Trouble with Biopython residue depth
proteins depth biopython residue
updated by Wayne Wayne • written by Anand KR • Anand KR
0 votes
2 replies
903 views
all genes have negative logFC edgeR
edger
updated by rfran010 • rfran010 • written by xiaoyongli407 • xiaoyongli407
0 votes
2 replies
1.3K views
Split vcf file to fit tbi requirements
snp haplotypecaller vcf gatk
written by cassandriatayfernandez • cassandriatayfernandez
1 vote
0 replies
581 views
Dealing with indels in a fungal ITS2 MSA
indels its2 msa alignment
written by Sergio A.S. • Sergio A.S.
0 votes
1 reply
1.2K views
GPU-accelerated multiple sequence alignment tools
multiple-sequence-alignment
updated by Ram Ram • written by jet • jet
0 votes
6 replies
2.2K views
WGCNA package.
rna-seq wgcna
written by Jaber • Jaber
0 votes
0 replies
428 views
Paired splsda
splsda
updated by Ram Ram • written by michelafrancesconi9 • michelafrancesconi9
0 votes
3 replies
1.1K views
Mapping to transcriptome without gtf annotation
transcriptome mapping assembly
updated by Michael Dondrup Michael Dondrup • written by ZuelTech • ZuelTech
0 votes
1 reply
929 views
Getting data from NCBI using Python
ensembl pyensembl rna-seq
updated by Ram Ram • written by Quân • Quân
1 vote
6 replies
2.3K views
Mapping all 32-mers within Hamming Distance = 3
hamming alignment kmer ngs short
updated by mourisl • mourisl • written by giova34 • giova34
0 votes
0 replies
605 views
How to work with Low allele Depth Variants in Strelka Variant caller
strelka allelic-depth low-gqx
updated by Ram Ram • written by abhishekghadge • abhishekghadge
0 votes
1 reply
1.7K views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta-analysis metal gwas
updated by Ram Ram • written by ymberzal • ymberzal
0 votes
0 replies
2.1K views
METAL meta-analysis software crash
metal meta-analysis gwas
updated by Ty • Ty • written by ydadmehr • ydadmehr
0 votes
3 replies
1.1K views
cutadapt not working when calling in a bash code with qsub
qsub trim cutadpat
updated by ATpoint ATpoint • written by Meghan.T • Meghan.T
0 votes
3 replies
1.7K views
Removing features from RNA assay in seurat
r seurat sc-rna-seq
updated by yura.grabovska • yura.grabovska • written by Varun Gupta Varun Gupta
0 votes
0 replies
758 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 Physalia-courses
0 votes
6 replies
2.0K views
miRNAseq - over-presented sequence in negative control
mirnaseq adaptor dimer
updated by Ant • Ant • written by MH85 • MH85
0 votes
0 replies
519 views
Differential expression analysis from .chp files with Limma
expression limma iontorrent differential
written by Rogerio Ribeiro • Rogerio Ribeiro
0 votes
2 replies
1.7K views
Genome Polishing nextPolish
nextpolish2 nextpolish pilon racon
written by SomeOne • SomeOne
0 votes
1 reply
768 views
co-occurrence matrix from my VCF file
co-occurrence vcf
updated by robben • robben • written by HarperReed • HarperReed
0 votes
6 replies
3.4K views
Center multiple pheatmap
pheatmap patchwork
updated by yura.grabovska • yura.grabovska • written by 5utr 5utr
0 votes
3 replies
1.3K views
creat histogram in R
r ggplot2 hist
updated by ATpoint ATpoint • written by G.S • G.S
0 votes
5 replies
2.1K views
constructing gene-based pangenome from orthofinder output file
orthofinder pan-genome
updated by Dunois • Dunois • written by Bushra Bibi Bushra Bibi
0 votes
6 replies
1.8K views
Genome Assembly Sorting
genome assembly sorting
updated by GenoMax GenoMax • written by SomeOne • SomeOne
0 votes
3 replies
1.6K views
Install PacBio lima via conda fails
conda
updated by colindaven colindaven • written by michael.flower.14 • michael.flower.14
0 votes
3 replies
1.1K views
human_variation_vcf
baserecalibrator
written by runfreely2 • runfreely2
0 votes
2 replies
875 views
How to interpret Eigengene dendrongram results
eigengene dendrogram
written by nuorain • nuorain
0 votes
24 replies
6.7K views
GTF file
cellranger-arc gtf cellranger-arc-2.0.2
written by IrK IrK
1 vote
6 replies
1.6K views
Explanation of DESeq factor leveling
deseq
written by bthom • bthom
0 votes
1 reply
672 views
Allele frequency plot : imputed vs reference panel variants
imputation genotyping reference
updated by BlastedBadger BlastedBadger • written by hello_genome • hello_genome
0 votes
1 reply
636 views
rRNA contamination after filtering
qc contamination ribosomal-rna
updated by GenoMax GenoMax • written by sleepystudent • sleepystudent
1 vote
0 replies
595 views
Repeated ensembl IDs in microarray DEG analysis
r annotation degs microarray limma
written by Pereira G • Pereira G
0 votes
2 replies
1.1K views
How to filter annotated genes overlapping with TE/repeat element?
genome gene annotation
written by Yao • Yao
6 votes
13 replies
3.8K views
Forum: How to do datamining in bioinformatics
data-mining
updated by LauferVA LauferVA • written by Biomed-jeh • Biomed-jeh
1 vote
3 replies
3.2K views
Why parametric linkage analysis on Merlin gives zero "0" LOD score?
snp alohomora merlin
updated by Ram Ram • written by eDNAuRNA • eDNAuRNA
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 • Javi.villegas21
0 votes
1 reply
728 views
What are the epithelial cells subtype in esophagus tissue ?
python scanpy anndata single-cell
updated by ATpoint ATpoint • written by AlexStar • AlexStar
0 votes
0 replies
670 views
News: ONLINE COURSE – Genome Assembly and Annotation (GAAA01)
annotation genome assembly genomics
updated by GenoMax GenoMax • written by oliverhooker oliverhooker
0 votes
1 reply
804 views
News: Course: Single-cell RNA-seq analysis with R/Bioconductor
bioconductor single-cell-rnaseq
updated by yura.grabovska • yura.grabovska • written by Physalia-courses Physalia-courses
0 votes
0 replies
727 views
Query regarding interpretation of VCF from variant calling (SVs) using vg giraffe workflow
pangenome giraffe vcf vg
written by s_135 • s_135
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 • s_135
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