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0 votes
2 replies
1.0K views
Base Quality Score Recalibration with different reference genome
snps gatk bqsr rna-seq
written by dtnondorf • dtnondorf
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 • Chris Dean • written by sovrappensiero • sovrappensiero
0 votes
2 replies
1.2K views
RNA-seq data for deep learning classification
rna-seq
written by yahn • yahn
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 • Qroid
0 votes
1 reply
2.1K views
Loss of 'var' using concatenation of AnnData objects
scanpy anndata
updated by Hugo • Hugo • written by Rachel • Rachel
0 votes
1 reply
697 views
Provean help
variant provean
updated by Mensur Dlakic Mensur Dlakic • written by Arun Sai Kumar • Arun Sai Kumar
0 votes
1 reply
1.6K views
Download eQTL data of one specific gene for all tissues from GTEx
eqtl gtex
updated by bk11 • bk11 • written by Jeol • Jeol
0 votes
7 replies
2.0K views
How does gene length effect the number of reads mapped
rna-seq cpm sequencing
written by Chen • Chen
0 votes
5 replies
1.8K views
Problem with data downloaded from Short Reads Archive (SRA)
sra dada2 metabarcoding
updated by atharvakarkare14 • atharvakarkare14 • written by Begonia_pavonina • Begonia_pavonina
0 votes
8 replies
3.0K views
Downsampling long-read BAM files
nanopore bam qc ont downsampling
written by eebloom • eebloom
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 ATpoint • written by alifafiq1 • alifafiq1
0 votes
0 replies
415 views
Use of annotation of integrated Seurat object in single sample
seurat
written by Nona • Nona
0 votes
0 replies
552 views
News: Beyond beginner R: Advancing your coding skills - September 16-19
advanced-coding programming r
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
1 reply
933 views
Subsetting and merging back Seurat Object brings different results
seurat
written by Nona • Nona
0 votes
0 replies
951 views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
ngs genomics post-doc r-loops
updated by Ram Ram • written by 4r-rtg • 4r-rtg
1 vote
1 reply
748 views
Discrepancy in read counts from fastq
downsampling fastq
updated by Ram Ram • written by marco.barr • marco.barr
0 votes
0 replies
669 views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
written by Vijith • Vijith
0 votes
14 replies
4.2K views
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated by GenoMax GenoMax • written by nicole.kavanagh • nicole.kavanagh
0 votes
1 reply
1.4K views
Is there a way to increase the automatic label text size in Cytoscape?
cytoscape
updated by Scooter Scooter • written by avocado123 • avocado123
0 votes
0 replies
810 views
Combining Methylation Microarray data from different platforms
microarray dna epic 450k methylation
written by James • James
0 votes
1 reply
1.3K views
Basic stats in hierfstat
fst stats hierfstat
updated by mdav • mdav • written by Zoe • Zoe
0 votes
3 replies
1.1K views
Odd alignment question/finding
alignment
updated by barslmn • barslmn • written by poordumbsillyidiot • poordumbsillyidiot
0 votes
1 reply
752 views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
gatk recalibration
updated by GenoMax GenoMax • written by mgranada3 • mgranada3
0 votes
0 replies
544 views
Looking for the best way to interpret these data
rna-seq ontology go
updated by Ram Ram • written by Oscar • Oscar
0 votes
7 replies
2.9K views
Post-imputation plot
michigan-imputation-server quality-control
updated by LChart LChart • written by kl • kl
0 votes
1 reply
1.0K views
How to find overlap of clusters in two seurat porject
clustering seurat
updated by Adam • Adam • written by J • J
0 votes
3 replies
1.1K views
DESeq2 processing problems
deseq2 r
updated by ATpoint ATpoint • written by jagdish7921 • jagdish7921
0 votes
1 reply
1.6K views
cnetplot category names are too long
clusterprofiler rna-seq enrichplot cnetplot
updated by Ram Ram • written by carov • carov
0 votes
1 reply
720 views
Mutect2 for mitochondria variant discovery
mutect2 mitochondria
updated by Ram Ram • written by ernestine.kubi • ernestine.kubi
0 votes
0 replies
520 views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent bacteria circularise
written by VITALA • VITALA
0 votes
2 replies
978 views
POSSUM not working due to incompatible pssm file
fasta pse-pssm pssm possum
written by rianna.collins • rianna.collins
0 votes
1 reply
662 views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated by i.sudbery i.sudbery • written by Edmond • Edmond
0 votes
0 replies
627 views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
written by O.rka O.rka
0 votes
1 reply
1.4K views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated by Ram Ram • written by Dr Huma Naz • Dr Huma Naz
0 votes
2 replies
2.0K views
p-value in CIBERSORT
cibersort p-value
written by michelafrancesconi9 • michelafrancesconi9
0 votes
5 replies
1.5K views
Telescope issue
telescope rna-seq
updated by GenoMax GenoMax • written by eleven11 • eleven11
3 votes
6 replies
3.6K views
Programmatically retrieving positions of protein active site residues
uniprot pdb proteins
updated by me me • written by Mariana • Mariana
0 votes
1 reply
1.0K views
Adjust pvalue in R with different approach give me all different outcome
statistics r p-value
updated by Ram Ram • written by Jonathan Yoou • Jonathan Yoou
0 votes
2 replies
999 views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast pssm
written by Nafi • Nafi
0 votes
3 replies
1.2K views
What does 'bundle_uuid' refer to in this metadata sheet?
sra illumina geo metadata
updated by GenoMax GenoMax • written by jeffrey.maurer.informatics • jeffrey.maurer.informatics
0 votes
3 replies
1.7K views
ERROR When Using Ensembl Plants Biomart Wget API
biomart plant ensembl
written by Dora • Dora
0 votes
0 replies
786 views
News: Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
bionumpy python numpy
updated by Ram Ram • written by Chakri • Chakri
0 votes
2 replies
782 views
RNA editing sites based on DNA seq and RNA seq
rna-editing
written by Ahiad Chen Zion • Ahiad Chen Zion
0 votes
5 replies
1.7K views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
written by Riccardo • Riccardo
0 votes
0 replies
589 views
News: Online course: Meta-analysis in R - last 2 seats left
meta-analysis statistics r
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
0 replies
716 views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer mutect variant-calling gatk somatic-variants
updated by Ram Ram • written by Alexandros • Alexandros
0 votes
1 reply
778 views
unable to get feature count results
featurecounts
updated by Ram Ram • written by Ravita • Ravita
0 votes
3 replies
918 views
KEGG Pathways
r rna-seq
updated by Ram Ram • written by Sudip • Sudip
1 vote
6 replies
5.6K views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton snp filter
updated by Andres • Andres • written by hermathena • hermathena
0 votes
0 replies
958 views
Seurat object reductions (PCA, UMAP,..) after subsetting data
seurat
written by Nona • Nona
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