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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 5.6K • | written by Pallondyle 0
0 votes
5 replies
1.6K views
How to compile Multiz
lastz github multiz
updated by Pierre Lindenbaum 17K • | written by Santex 0
1 vote
2 replies
1.0K views
Converting bam to sam using htslib C++ api
bam htslib sam
updated by Pierre Lindenbaum 17K • | written by Uveyik 8
1 vote
1 reply
1.9K views
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
rna-seq
updated by Nat.Nataren 10 • | written by roxana 1
0 votes
0 replies
611 views
Issues with EnrichPathway Barplot in Reactome Pathway Analysis
rna-seq
written by roxana 1
0 votes
0 replies
758 views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp vcf gatk
written by CRL-CHAR 0
0 votes
2 replies
1.1K views
MarkDuplicatesSpark GATK flags for overcoming space issues
gatk
written by ChumBucket2024 1
0 votes
6 replies
2.0K views
FastQC and HISAT2
hisat2 fastqc rna-seq
updated by GenoMax 16K • | written by Jaber 3
0 votes
0 replies
605 views
News: An Introduction to Nanopore direct RNA sequencing
cdna rna-seq nanopore
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
2 replies
1.2K views
Can't run CrossMap
crossmap
written by Muhammad 0
0 votes
2 replies
863 views
ChromHMM bed file annotation
chromhmm annotation
written by sk_24 0
0 votes
2 replies
962 views
Numreads from samtools for Differential Expression
samtools featurecounts rna-seq deseq numreads
updated by Ram 4.5K • | written by pedroc.c 0
1 vote
0 replies
949 views
Job: Graduate student positions (2-year Master's program) to conduct research in bioinformatics
graduate-student masters-program
updated by Ram 4.5K • | written by Michael Gruenstaeudl 1
0 votes
0 replies
588 views
Confusing Pathway Analysis Results from DAVID
david reactome kegg
written by saamhasan55 3
0 votes
1 reply
797 views
Can someone install me (remotely) Amber24?
amber24
updated by Ram 4.5K • | written by Belén 0
0 votes
5 replies
2.0K views
Issue understanding ATAC-seq PCA
atac-seq pca
updated by LChart 518 • | written by Ronin 1
0 votes
0 replies
648 views
ChromHMM
annotation promoter chromhmm
written by sk_24 0
0 votes
0 replies
456 views
Unable to analyse with cytoscape plugin bingo
bingo
written by bookorg 2
0 votes
4 replies
1.3K views
No available matched normal for Mutect2 GATK
gatk
written by shems2001 0
0 votes
6 replies
1.8K views
Kraken classified based on 1 mer
kraken2
updated by colindaven 844 • | written by Jyoti 0
0 votes
3 replies
2.2K 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 10K • | written by Joe Kherery 15
0 votes
2 replies
1.3K views
Trimmomatic 0.39 fails for adapters
trimmomatic
updated by Istvan Albert 10K • | written by pinheirofabiano 14
0 votes
2 replies
1.6K views
Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs across multiple samples
mapq bam coverage
written by Novice 1
0 votes
3 replies
1.4K views
Are tens of DEGs still biologically meaningful?
deg differential-expression-analysis
updated by DGTool 30 • | written by FedeXandeR 2
1 vote
1 reply
962 views
Extract bam file to sam inside code?
bam sam
updated by Pierre Lindenbaum 17K • | written by Uveyik 8
0 votes
1 reply
1.1K views
invalid class “DimReduc” object in `ArchR`
archr
updated by Bastien Hervé 680 • | written by Dan 18
0 votes
1 reply
946 views
Extracting column from one seurat object based on common column and adding to the other object
r seurat
updated by bk11 312 • | written by Varun Gupta 129
0 votes
3 replies
1.2K views
Pedigree information
pedigree plink king
updated by bk11 312 • | written by heureuse 1
0 votes
4 replies
1.7K views
How can I call somatic CNV in tumor and matched normal sample
tumor normal somatic-cnv
updated by Ram 4.5K • | written by Smilesky 0
1 vote
2 replies
1.0K views
How far pangenome from being the mainstream?
pangenome
updated by dsull 781 • | written by guntul 4
0 votes
0 replies
639 views
Bandage visualization of the transcriptome
trinity transcriptomics bandage rna-seq
updated by Ram 4.5K • | written by Lada 6
0 votes
1 reply
862 views
Looking for ressource/database of gene expression matrix for PDX mapped over human AND mouse
database pdx
written by ZheFrench 60
0 votes
14 replies
5.2K views
RNA-Seq mutation calling without germline data
rna-seq mutation
updated by littlebioinformatician 0 • | written by marionette.kent 0
0 votes
0 replies
453 views
Can't merge snATAC samples
snatac
written by myoui3122010 3
0 votes
12 replies
11K views
how to run freebayes in multi-thread
vcf freebayes multi-thread
updated by GenoMax 16K • | written by marongiu.luigi 79
1 vote
0 replies
619 views
News: Landscape Genomics course in Poland (January 20-24)
r localadaptation sambada landscapegenomics lfmm
written by Physalia-courses 281
0 votes
1 reply
974 views
PennCNV step1.1 error
xml apt-probeset-genotype penncnv cel apt
updated by Volter 0 • | written by jaredgichohi 0
2 votes
11 replies
3.1K views
Tool: A simple and lightweight tool for filtering csv file wirtten in Rust
gtf tab gff vcf csv
updated by Matthias Zepper 524 • | written by dwpeng 14
0 votes
1 reply
2.9K views
How can I convert a MAF of HAL (from cactus-hal2maf) to Multiple FASTA?
maf cactus
written by Mimi33 3
0 votes
4 replies
2.7K views
generating transcript to gene mapping with unhelpful GFF3 file
salmon rnaseq transcriptome gff3
updated by jayeshkumarsundaram 1 • | written by thomas.welch 5
0 votes
0 replies
506 views
Pseudohaplotype assembly with Hifiasm and sex chromosomes from XY specimen
hifiasm
written by acarter 0
0 votes
5 replies
7.5K views
How does edgeR's filterByExpr work?
edger
updated by Gordon Smyth 916 • | written by Haad 0
0 votes
1 reply
704 views
NeuronChat: identifyCommunicationPatterns_Neuron() error
r neuronchat
written by sooni 2
0 votes
4 replies
1.6K views
BaseRecalibrator User error.
gatk mutect2
updated by shems2001 0 • | written by ChumBucket2024 1
2 votes
2 replies
1.7K views
Difference between gam and sam/bam files?
bam pangenome gam sam
written by Uveyik 8
0 votes
1 reply
1.0K views
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
preimputaitoncheck
updated by bk11 312 • | written by guoweidora 0
1 vote
1 reply
1.0K views
Resources for learning Machine Learning to create clinical predictive models.
machine-learning ai
updated by Ram 4.5K • | written by egascon 6
0 votes
6 replies
2.3K views
Installing Mesquite on Linux
linux mesquite java phylogeny
written by Begonia_pavonina 22
0 votes
1 reply
830 views
Tools for assigning putative enhacers to respective genes
chip-seq
updated by jared.andrews07 1.9K • | written by alejandrocastillaibeas 2
0 votes
1 reply
941 views
GC content files download
gc-content
updated by GenoMax 16K • | written by KABILAN 13
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