This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
1 reply
1.0K views
DiffBind count function error related with BiocParallel and IRanges
dba chipseq iranges diffbind
written by buffealo • buffealo
0 votes
1 reply
686 views
Gene expression relational database
relational-database gene-expression
updated by Ram Ram • written by Daniela Alejandra • Daniela Alejandra
0 votes
3 replies
1.5K views
Error during batch correction/PCA
rna-seq batch-effect
written by Eduardo Oñate • Eduardo Oñate
0 votes
7 replies
1.8K views
Mendelian precison
cnv trios mendelian-precision
updated by Ram Ram • written by heureuse • heureuse
0 votes
6 replies
2.6K views
Using BBtools to remove polyGs in Illumina data
bbtools
updated by Brian Bushnell Brian Bushnell • written by hpapoli hpapoli
0 votes
2 replies
1.0K views
Clarification on UMI Length in FASTQ File after Trimming with fastp
umi adapter
updated by GenoMax GenoMax • written by daffodil • daffodil
0 votes
8 replies
2.0K views
HTseq count issue, not aligning to features
htseq hisat2 rna-seq
written by boone5jones • boone5jones
0 votes
11 replies
2.9K views
Sankey + dot plot
r sankey gene-ontology go
updated by dthorbur dthorbur • written by Sofia • Sofia
0 votes
3 replies
1.6K views
How to convert CSV format to VCF using Python?
vcf csv python
updated by Ram Ram • written by Mohadese • Mohadese
1 vote
4 replies
1.6K views
When to use integration with scRNASeq
r seurat scrna-seq
updated by Bastien Hervé Bastien Hervé • written by Varun Gupta Varun Gupta
0 votes
0 replies
453 views
Annotating WGS Metagenome assemblies
metagenomics assembly metagenome annotation
written by naveedhasan2000 • naveedhasan2000
0 votes
13 replies
3.3K views
featureCounts segmentation fault
featurecounts pipeline rna-seq
written by Jaber • Jaber
0 votes
2 replies
1.3K views
how to get visium HD dataset with its information
spatial visiumhd transcriptomics scanpy
updated by Nat.Nataren • Nat.Nataren • written by Genomancer • Genomancer
1 vote
10 replies
3.8K views
Using GEOquery
r geo ncbi
updated by Ram Ram • written by Aryan • Aryan
0 votes
4 replies
2.2K views
Performing Needleman-Wunsch Global Alignment for multiple mutant proteins against wild-type
global-alignment needleman-wunsch
updated by Istvan Albert Istvan Albert • written by VolEr • VolEr
0 votes
2 replies
1.1K views
Merging bfiles
fam plink bfile bed
written by aj123 aj123
1 vote
1 reply
826 views
Generally how are non-canonical chromosomes treated in human variation studies
variants sv assembly wgs
updated by GenoMax GenoMax • written by eebloom • eebloom
0 votes
8 replies
2.6K views
Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, and intron only
rna-seq featurecounts
written by Ian Ian
0 votes
0 replies
638 views
Differences in DeepTools Heatmap Resolution Driven by Bed File
deeptools heatmaps atacseq
written by gcooper1245 • gcooper1245
7 votes
9 replies
3.7K views
Forum: The Evolution of NGS: What’s New and What’s Next?
ngs
updated by GenoMax GenoMax • written by lakhujanivijay lakhujanivijay
0 votes
0 replies
739 views
How to do multiz alignment locally
axtchain lastz multiz
updated by GenoMax GenoMax • written by Santex • Santex
0 votes
0 replies
454 views
Significant difference in SNV count between replicates
vcf mutations wes snv
written by dana • dana
0 votes
15 replies
3.2K views
I have encountered some bugs in transcriptome analysis using STAR and RSEM.
star rsem
updated by Michael Dondrup Michael Dondrup • written by Pallondyle • Pallondyle
0 votes
5 replies
1.5K views
How to compile Multiz
lastz github multiz
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Santex • Santex
1 vote
2 replies
1.0K views
Converting bam to sam using htslib C++ api
bam htslib sam
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Uveyik • Uveyik
1 vote
1 reply
1.9K views
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
rna-seq
updated by Nat.Nataren • Nat.Nataren • written by roxana • roxana
0 votes
0 replies
586 views
Issues with EnrichPathway Barplot in Reactome Pathway Analysis
rna-seq
written by roxana • roxana
0 votes
0 replies
747 views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp vcf gatk
written by CRL-CHAR • CRL-CHAR
0 votes
2 replies
1.1K views
MarkDuplicatesSpark GATK flags for overcoming space issues
gatk
written by ChumBucket2024 • ChumBucket2024
0 votes
6 replies
1.9K views
FastQC and HISAT2
hisat2 fastqc rna-seq
updated by GenoMax GenoMax • written by Jaber • Jaber
0 votes
0 replies
595 views
News: An Introduction to Nanopore direct RNA sequencing
cdna rna-seq nanopore
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
2 replies
1.2K views
Can't run CrossMap
crossmap
written by Muhammad • Muhammad
0 votes
2 replies
845 views
ChromHMM bed file annotation
chromhmm annotation
written by sk_24 • sk_24
0 votes
2 replies
945 views
Numreads from samtools for Differential Expression
samtools featurecounts rna-seq deseq numreads
updated by Ram Ram • written by pedroc.c • pedroc.c
1 vote
0 replies
932 views
Job: Graduate student positions (2-year Master's program) to conduct research in bioinformatics
graduate-student masters-program
updated by Ram Ram • written by Michael Gruenstaeudl • Michael Gruenstaeudl
0 votes
0 replies
583 views
Confusing Pathway Analysis Results from DAVID
david reactome kegg
written by saamhasan55 • saamhasan55
0 votes
1 reply
784 views
Can someone install me (remotely) Amber24?
amber24
updated by Ram Ram • written by Belén • Belén
0 votes
5 replies
2.0K views
Issue understanding ATAC-seq PCA
atac-seq pca
updated by LChart LChart • written by Ronin • Ronin
0 votes
0 replies
636 views
ChromHMM
annotation promoter chromhmm
written by sk_24 • sk_24
0 votes
0 replies
447 views
Unable to analyse with cytoscape plugin bingo
bingo
written by bookorg • bookorg
0 votes
4 replies
1.3K views
No available matched normal for Mutect2 GATK
gatk
written by shems2001 • shems2001
0 votes
6 replies
1.8K views
Kraken classified based on 1 mer
kraken2
updated by colindaven colindaven • written by Jyoti • Jyoti
0 votes
3 replies
2.1K views
Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized RNA-Seq Data
dese2 cbioportal rna-seq limma
updated by Istvan Albert Istvan Albert • written by Joe Kherery Joe Kherery
0 votes
2 replies
1.2K views
Trimmomatic 0.39 fails for adapters
trimmomatic
updated by Istvan Albert Istvan Albert • written by pinheirofabiano • pinheirofabiano
0 votes
2 replies
1.5K views
Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs across multiple samples
mapq bam coverage
written by Novice • Novice
0 votes
3 replies
1.4K views
Are tens of DEGs still biologically meaningful?
deg differential-expression-analysis
updated by DGTool • DGTool • written by FedeXandeR • FedeXandeR
1 vote
1 reply
944 views
Extract bam file to sam inside code?
bam sam
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Uveyik • Uveyik
0 votes
1 reply
1.0K views
invalid class “DimReduc” object in `ArchR`
archr
updated by Bastien Hervé Bastien Hervé • written by Dan • Dan
0 votes
1 reply
918 views
Extracting column from one seurat object based on common column and adding to the other object
r seurat
updated by bk11 • bk11 • written by Varun Gupta Varun Gupta
0 votes
3 replies
1.2K views
Pedigree information
pedigree plink king
updated by bk11 • bk11 • written by heureuse • heureuse
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