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1 vote
1 reply
877 views
Testing the effect of the salinity water on abundance estimates
salinity
updated by ATpoint 9.1K • | written by Thibaut 1
0 votes
6 replies
2.2K views
How can I see probe IDs in a microarray?
r microarray probe affymetrix
written by wyt1995 4
0 votes
1 reply
908 views
Whole genome assembly
genome-assembly
updated by Ram 4.5K • | written by manaswiniparija3 6
0 votes
1 reply
672 views
Fish_genome_assembly
bgseq longreads oxfordnanopre hybridassembly
updated by dthorbur 350 • | written by manaswiniparija3 6
0 votes
0 replies
741 views
Annotating Seurat samples when merging objects
single seurat cell rnaseq
written by Gerard 2
1 vote
0 replies
777 views
News: shournal: A Tool for Bioinformaticians to Boost Research Reproducibility
reproducability terminal bash
written by David Langenberger 1.1K
0 votes
6 replies
2.3K views
Rooting phylogenetic trees in R using Treeio's root function: Trees don't seem to root.
r mrbayes
written by lingxue 0
0 votes
4 replies
1.4K views
Differential analysis using R
dna methylation
updated by Michael Dondrup 5.6K • | written by maryak 2
0 votes
1 reply
824 views
How to determine if a somatic mutation alters transcription factor binding site?
cancer motif tfbs somatic-mutation
updated by Ram 4.5K • | written by ConvolutedGenome 6
0 votes
1 reply
890 views
Protein protein interaction network
interaction protein network
updated by dthorbur 350 • | written by Tomk 0
0 votes
7 replies
1.8K views
Error "ckalloc: request for negative space" about multiz
multiz
written by marh32 0
0 votes
3 replies
1.7K views
How to analyze DEGs in scRNA-seq data?
deg single-cell scrna-seq rna-seq
updated by Ram 4.5K • | written by kayah 2
2 votes
4 replies
3.3K views
How to call mitochondrial SNP?
snp mitochondrial
updated by Ram 4.5K • | written by hxlei613 11
0 votes
2 replies
1.9K views
GATK's new best practice for mitochondrial variant calling
snp sequencing
updated by sriram_pharm 0 • | written by lovelysunzt 0
0 votes
2 replies
1.5K views
scRNAseq output generated using STARsolo has gene_id rather than gene_name
starsolo rnaseq seurat single-cell
written by Lauren 0
0 votes
0 replies
519 views
Help plotting enrichment results - kegg terms
enrichment-analysis kegg
updated by Ram 4.5K • | written by DByter 0
0 votes
0 replies
542 views
DWGSIM incorrectly mapped reads
dwgsim rna-seq mapping transcriptomics
written by cst_rmrz 0
0 votes
6 replies
2.1K views
Forum: You have 3 days of zero obligations and expansive resources. What are you building?
hypothetical thought-experiment
written by jared.andrews07 1.9K
0 votes
8 replies
2.8K views
Finding insert sequences using long reads
insert-sequences nanopore long-read-assembly
updated by Anand Rao 65 • | written by bvm 2
0 votes
2 replies
5.1K views
Align dorado output to reference
minimap2 bam nanopore dorado
updated by colindaven 844 • | written by njornet 2
0 votes
6 replies
1.9K views
Odd behaviour - NCBI Eutils
ncbi eutils esearch eutilities efetch
updated by GenoMax 16K • | written by npb27 2
0 votes
2 replies
1.1K views
DiffBind issue in identification of differentially enriched peaks between two conditions
diffbind chip-seq
written by accibio 2
0 votes
1 reply
819 views
News: Integrated Genome Browser (IGB) Office Hours
integrated-genome-browser igb
updated by Ram 4.5K • | written by IGB Helper 0
0 votes
0 replies
424 views
Reactome isChimeric attribute
reactome
written by Ana 2
0 votes
5 replies
1.7K views
loop string set
python stringset
updated by rpolicastro 1.3K • | written by aj123 14
0 votes
0 replies
805 views
issue with the Arima genomics pipeline for Hi-C scaffolding
plant pacbio assembly genome hi-c
written by rj.rezwan 2
0 votes
1 reply
1.1K views
How to use `bai_file`/`sample_id` (cardinality=10) and `bin_id` (cardinality=2875) much efficiently here?
nextflow
written by Đặng Hải Đăng 0
0 votes
3 replies
2.4K views
samtools view: error reading file
samtools bowtie2
updated by bioinfo_ga 7 • | written by ray 0
1 vote
14 replies
9.0K views
Trouble with bedtools getfasta
bedtools getfasta
updated by ad.amkl.a.r.i.s.4. 0 • | written by gkunz 3
0 votes
0 replies
526 views
Interpret ImpulseDE2 output?
rna-seq
written by CTLong 14
0 votes
3 replies
1.2K views
RNA-seq bam file normalization
rna-seq bam normalization
updated by dsull 781 • | written by maplewj 2
0 votes
1 reply
1.0K views
FeatureCounts has duplicate Gene names
rna-seq
updated by GenoMax 16K • | written by Confused_human 3
0 votes
0 replies
738 views
Tutorial for COSMIC? Any way to calculate VAF?
cosmic
written by gernophil 15
0 votes
0 replies
696 views
Forum: What other data types and pipelines you would like to see from the Genomics Data Commons (GDC)
gdc tcga genomics-data-commons
updated by Ram 4.5K • | written by Zhenyu Zhang 130
0 votes
0 replies
538 views
Characterization of mutations in vcf files
mutations vcf characterization
written by RUBEM 0
0 votes
0 replies
815 views
News: Online course: Network Analysis in Systems Biology with R/Bioconductor
r rna-seq network-analysis bioconductor systems-biology
updated by Ram 4.5K • | written by Physalia-courses 281
1 vote
1 reply
1.0K views
How to download raw data such as fastq file from MG-RAST?
mg-rast
updated by GenoMax 16K • | written by Adi 2
0 votes
1 reply
719 views
Tumorportal
tumorportal
updated by Ram 4.5K • | written by ananta.kapoor 0
0 votes
0 replies
591 views
Beagle don't recognize parents
beagle
written by Michal Frenkel 3
0 votes
4 replies
2.6K views
If the mane transcript isn't available should you use the canonical transcript?
ensembl mane gnomad canonical
written by hello_bioinf 25
0 votes
2 replies
2.9K views
RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or 'exon'
featurecounts ncbi ensembl gff rnaseq
updated by Gordon Smyth 916 • | written by BioinfGuru 214
0 votes
7 replies
2.7K views
MA graphs for EdgeR and Voom vary
edger transcriptomics graph voom ma
updated by Gordon Smyth 916 • | written by af1065 0
0 votes
2 replies
1.9K views
Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatics Methods Post Biology Undergrad
literature limma
updated by Ram 4.5K • | written by Serij´s 0
0 votes
15 replies
4.0K views
Novel sparse optimisation for high accuracy cancer classification on the 33-cancer TCGA gene-expression dataset
tcga pancan cancer-classification gene-expression
updated by Jeremy Leipzig 2.3K • | written by Mark Reilly 2
0 votes
3 replies
1.4K views
blast in python
blast python
updated by Wayne 208 • | written by brunofelicianodeomena 0
0 votes
4 replies
1.8K views
Salmon
salmon seurat gene-expression
updated by Ram 4.5K • | written by Bizhan 0
0 votes
5 replies
2.9K views
long view SNPs in vcf file
bcftools variant-calling snp freebayes vcftools
updated by yzliu01 1 • | written by young_bioinformatician 25
0 votes
1 reply
854 views
How to get population specific SNPs from a vcf file
specific snps population
updated by Pierre Lindenbaum 17K • | written by 291796256 0
0 votes
0 replies
606 views
WGCNA module of interest, correlate GENES with trait
wgcna
written by Anders 0
0 votes
0 replies
921 views
Trouble running GSEA analysis on log2 fold change values of RNA-seq data
rnaseq gsea rnk
written by trkfs 1
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