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0 votes
0 replies
792 views
issue with the Arima genomics pipeline for Hi-C scaffolding
plant pacbio assembly genome hi-c
written by rj.rezwan • rj.rezwan
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 • Đặng Hải Đăng
0 votes
3 replies
2.4K views
samtools view: error reading file
samtools bowtie2
updated by bioinfo_ga • bioinfo_ga • written by ray • ray
1 vote
14 replies
8.9K views
Trouble with bedtools getfasta
bedtools getfasta
updated by ad.amkl.a.r.i.s.4. • ad.amkl.a.r.i.s.4. • written by gkunz • gkunz
0 votes
0 replies
522 views
Interpret ImpulseDE2 output?
rna-seq
written by CTLong • CTLong
0 votes
3 replies
1.2K views
RNA-seq bam file normalization
rna-seq bam normalization
updated by dsull dsull • written by maplewj • maplewj
0 votes
1 reply
1.0K views
FeatureCounts has duplicate Gene names
rna-seq
updated by GenoMax GenoMax • written by Confused_human • Confused_human
0 votes
0 replies
726 views
Tutorial for COSMIC? Any way to calculate VAF?
cosmic
written by gernophil • gernophil
0 votes
0 replies
695 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 Ram • written by Zhenyu Zhang Zhenyu Zhang
0 votes
0 replies
534 views
Characterization of mutations in vcf files
mutations vcf characterization
written by RUBEM • RUBEM
0 votes
0 replies
809 views
News: Online course: Network Analysis in Systems Biology with R/Bioconductor
r rna-seq network-analysis bioconductor systems-biology
updated by Ram Ram • written by Physalia-courses Physalia-courses
1 vote
1 reply
1.0K views
How to download raw data such as fastq file from MG-RAST?
mg-rast
updated by GenoMax GenoMax • written by Adi • Adi
0 votes
1 reply
715 views
Tumorportal
tumorportal
updated by Ram Ram • written by ananta.kapoor • ananta.kapoor
0 votes
0 replies
587 views
Beagle don't recognize parents
beagle
written by Michal Frenkel • Michal Frenkel
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 • hello_bioinf
0 votes
2 replies
2.8K views
RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or 'exon'
featurecounts ncbi ensembl gff rnaseq
updated by Gordon Smyth Gordon Smyth • written by BioinfGuru BioinfGuru
0 votes
7 replies
2.7K views
MA graphs for EdgeR and Voom vary
edger transcriptomics graph voom ma
updated by Gordon Smyth Gordon Smyth • written by af1065 • af1065
0 votes
2 replies
1.8K views
Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatics Methods Post Biology Undergrad
literature limma
updated by Ram Ram • written by Serij´s • Serij´s
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 Jeremy Leipzig • written by Mark Reilly • Mark Reilly
0 votes
3 replies
1.4K views
blast in python
blast python
updated by Wayne Wayne • written by brunofelicianodeomena • brunofelicianodeomena
0 votes
4 replies
1.7K views
Salmon
salmon seurat gene-expression
updated by Ram Ram • written by Bizhan • Bizhan
0 votes
5 replies
2.9K views
long view SNPs in vcf file
bcftools variant-calling snp freebayes vcftools
updated by yzliu01 • yzliu01 • written by young_bioinformatician young_bioinformatician
0 votes
1 reply
840 views
How to get population specific SNPs from a vcf file
specific snps population
updated by Pierre Lindenbaum Pierre Lindenbaum • written by 291796256 • 291796256
0 votes
0 replies
598 views
WGCNA module of interest, correlate GENES with trait
wgcna
written by Anders • Anders
0 votes
0 replies
910 views
Trouble running GSEA analysis on log2 fold change values of RNA-seq data
rnaseq gsea rnk
written by trkfs • trkfs
1 vote
4 replies
2.6K views
Snakemake: how to define output from a dictionary according to wildcard
wildcards snakemake dictionary
written by ema • ema
0 votes
2 replies
1.4K views
Elastic BLAST vs. BLAST cloud
blast
updated by Yannick Wurm Yannick Wurm • written by Joseph Kashmer • Joseph Kashmer
0 votes
2 replies
1.3K views
Alphafold2 Colab
alphafold
updated by dthorbur dthorbur • written by Preeti • Preeti
0 votes
2 replies
2.6K views
Want to uninstall apache ant, can't find the install
ubuntu apache ant
written by Matthew • Matthew
0 votes
4 replies
1.7K views
How to download Accession List from NCBI on CLI?
cli ncbi python
updated by GenoMax GenoMax • written by Cam • Cam
0 votes
2 replies
1.5K views
Job: Junior Research Software Engineer/ Research Software Engineer - web resources for virology
software developer web virology
written by Joseph Hughes Joseph Hughes
0 votes
0 replies
568 views
help a general guideline of bioinformatics strategy to analize gut metagenome virome data from stool samples
gut-virome
updated by Ram Ram • written by Israel • Israel
0 votes
3 replies
1.4K views
Genes with multiple chromosome locations
gene annotation loci alternative
updated by Alex Reynolds Alex Reynolds • written by Pac314 • Pac314
0 votes
2 replies
1.2K views
WGCNA, correlation with trait data from different individuals
wgcna
written by boczniak767 boczniak767
0 votes
2 replies
1.3K views
Forum: What's the state of the art in bacterial whole genome alignment?
whole genome alignment mauve
written by Dave Carlson Dave Carlson
0 votes
1 reply
875 views
Where to find a GTF, GFF, or SAF for RheMac2 genome
annotations
updated by GenoMax GenoMax • written by Sillyman • Sillyman
0 votes
1 reply
1.1K views
Huge TPM values in some tissues of an expression atlas
gene expression
updated by jared.andrews07 jared.andrews07 • written by lessismore lessismore
0 votes
1 reply
1.3K views
How is strandedness preserved with PCR (DNA/RNA-seq)
pcr strandedness sequencing
updated by Carlo Yague Carlo Yague • written by Sotiris • Sotiris
0 votes
0 replies
534 views
Isolate somatic variants from VCF files coming from cell-free DNA
ngs analysis vcf somaticvariants germlinevriants
written by eleni.psar • eleni.psar
1 vote
2 replies
1.1K views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
transcriptomics single-cell
updated by Ram Ram • written by Daddy • Daddy
0 votes
13 replies
8.7K views
How to convert raw Nanopore R9 fast5 files to fastq files ?
dorado fast5 basecalling nanopore
updated by lieven.sterck lieven.sterck • written by Lélé • Lélé
0 votes
4 replies
1.5K views
Rna editing
annotation transcriptome rna-seq
written by RUBEM • RUBEM
0 votes
0 replies
886 views
Job: PhD offer metabarcoding plant insect interaction in agricultural fields in Germany
metabarcoding enthomology botany
written by b.gemeinholzer • b.gemeinholzer
0 votes
6 replies
2.0K views
Selection of GTF file from gencode
star
updated by GenoMax GenoMax • written by Nodilan • Nodilan
0 votes
3 replies
1.2K views
GnomAD
gnomad
written by ananta.kapoor • ananta.kapoor
13 votes
38 replies
50K views
Illumina Instrument Type from fastq?
fastq
updated by GenoMax GenoMax • written by andrew.j.skelton73 andrew.j.skelton73
1 vote
3 replies
1.2K views
Integrate Chipseq and Atacseq data?
atac-seq chip-seq
written by RD • RD
0 votes
0 replies
904 views
Guidance Needed: Matching Cancer-Specific Alterations with ATAC-seq Genomic Coordinates
alignment atac-seq cancer
written by davoudamirimehr • davoudamirimehr
1 vote
1 reply
3.7K views
TopMed freeze8 reference panel download
reference panel topmed imputation genotype
updated by fukun • fukun • written by dtzhu337 • dtzhu337
0 votes
1 reply
960 views
Codon Usage Analysis
codon
updated by zx8754 zx8754 • written by jl056933 • jl056933
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