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0 votes
2 replies
926 views
Finding gtf file for safflower
gtf safflower
written by Bushra Bibi Bushra Bibi
0 votes
8 replies
3.9K views
Help in Log2 transform CPM count
r edger dge deseq2
updated by Ram Ram • written by G.S • G.S
0 votes
1 reply
1.1K views
Job: Postdoctoral Fellow in Machine Learning for Neuroimaging Genomics at University of Otago – Dunedin, New Zealand
human-genomics machine-learning neuroimaging
written by narun.pat • narun.pat
0 votes
1 reply
882 views
How to make local BLAST sequentially look through a large number of databases and generate a file for each
blast
updated by GenoMax GenoMax • written by nipayrhk • nipayrhk
0 votes
1 reply
2.7K views
Problems with overlapping variants in a vcf file
bcftools variant vcf
updated by Ram Ram • written by Buxus • Buxus
2 votes
1 reply
1.0K views
Removing / Excluding / Collapsing Overlapping Indels
bcftools genome vcf genotyping gatk
written by jon.klonowski jon.klonowski
0 votes
5 replies
2.7K views
GATK SelectVariants consider spanning/overlapping deletions as SNP
selectvariants snp gatk indel
updated by jon.klonowski jon.klonowski • written by cocchi.e89 cocchi.e89
0 votes
1 reply
641 views
Contrasting multiple tissues in DiffBind
diffbind chip-seq
updated by Ram Ram • written by aaron.varghese • aaron.varghese
0 votes
1 reply
817 views
Common SNP/variome-aware restriction digest generator for human genome
variome snp restriction-enzyme
updated by Ram Ram • written by hurfdurf hurfdurf
0 votes
4 replies
4.6K views
Create Seurat Object from matrix and two text files
single-cell rna-seq seurat
updated by blackbruce0405 • blackbruce0405 • written by Sky • Sky
0 votes
3 replies
1.2K views
Confusion during BARCODE MATCHING.
primers metagenomics barcode
updated by GenoMax GenoMax • written by Buket • Buket
0 votes
1 reply
1.8K views
Creating a signature matrix using CibersortX
cibersortx deconvolution
updated by jared.andrews07 jared.andrews07 • written by Aspire Aspire
0 votes
2 replies
2.2K views
Plotting LD heat map with plink.ld result
r
written by selplat21 • selplat21
1 vote
0 replies
836 views
What exactly is Biopython's alignment.score variable?
biopython
written by Tom • Tom
1 vote
0 replies
523 views
What happens to M-phase cells in single nucleus RNA-seq?
10x multiome snrnaseq
written by mpiersonsmela • mpiersonsmela
0 votes
4 replies
2.3K views
Interpretation of PRS scores calculated from PGS Catalog
prs pgs-catalog
updated by UnivStudent UnivStudent • written by Patrick • Patrick
0 votes
4 replies
1.3K views
Expression quantification = how is it possible that the amount of sequenced reads assigned to a specific gene/transcript
rna-seq quantification
updated by Bastien Hervé Bastien Hervé • written by mairena.hirschberg • mairena.hirschberg
0 votes
1 reply
864 views
Polygenic risk score percentile cutoff
gwas odds beta
updated by UnivStudent UnivStudent • written by endoplasmicreticulum12 • endoplasmicreticulum12
0 votes
1 reply
1.9K views
Calculating PRS from pre-computed PGS Catalog
gwas prs pgs
updated by UnivStudent UnivStudent • written by user230613 user230613
0 votes
1 reply
845 views
QC for UKB GWAS data
ukb gwas qc
updated by bk11 • bk11 • written by Mahnaz • Mahnaz
8 votes
9 replies
44K views
How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids?
extraction read 454 fastq fasta
updated by GenoMax GenoMax • written by Biomonika (Noolean) Biomonika (Noolean)
0 votes
0 replies
684 views
Can a Binary Signature Matrix Be Used in CIBERSORT for Deconvolution?
regression svm cibersort svr
written by DareDevil DareDevil
0 votes
3 replies
1.2K views
Manually creating a valid VCF File
vcf-validator vcf
updated by Bastien Hervé Bastien Hervé • written by Sara • Sara
0 votes
2 replies
1.5K views
Extraction of miRNA Sequences from Infernal cmscan Output Using Python
infernal assembly rna genome mirna
updated by massa.kassa.sc3na massa.kassa.sc3na • written by Vijith • Vijith
0 votes
12 replies
3.8K views
Forum: What bioinformatics codes would you use for performance benchmarking on a new system?
benchmarking
written by Dave Carlson Dave Carlson
1 vote
3 replies
2.2K views
Beagle imputation error
imputation beagle
written by PKW • PKW
0 votes
5 replies
2.4K views
BioPython - qblast() timeout every time, running from python shell
qblast biopython blast ncbi
written by Ryan • Ryan
0 votes
0 replies
781 views
News: Population Genomics course (online)
ngs populationgenomics introgression landscapegenomics gwas
written by Physalia-courses Physalia-courses
0 votes
6 replies
2.4K views
how to effectively pipe chromap into samtools view
samtools bash pipe
written by Matteo Ungaro • Matteo Ungaro
1 vote
1 reply
1.2K views
Batch correction of whole genome bisulfite methylation data
wgbs
updated by jlshi.nudt jlshi.nudt • written by irfanwustl • irfanwustl
0 votes
11 replies
3.1K views
How to solve DESeq2 Error in checkFullRank(modelMatrix) cause by biological replicates information?
deseq2 deseq
updated by swbarnes2 swbarnes2 • written by ace • ace
0 votes
5 replies
1.8K views
Best workflow for identification of isoforms and splice variants
isoforms rna-seq variants splice
updated by dsull dsull • written by Vojtěch • Vojtěch
0 votes
0 replies
557 views
does genomics_general.py need both invariant sites and variant sites to calculate pi, FST and DXY
genomics_general
written by Maxine • Maxine
0 votes
1 reply
845 views
CLC Genomics workbench and dbSNP VCF import
vcf
updated by GenoMax GenoMax • written by むらい • むらい
0 votes
0 replies
647 views
Adding and removing sequences in Repeatmasker library (modifying library)
repeatmasker genome repeats
updated by Ram Ram • written by MK • MK
0 votes
2 replies
1.1K views
Whole Metagenome Analysis
metagenomics
written by karthick • karthick
0 votes
1 reply
3.8K views
Clarification on WGCNA Module-Trait Correlations, Interpretation, and Functional Annotation
wgcna
updated by LChart LChart • written by Shaheer Syed • Shaheer Syed
2 votes
2 replies
1.1K views
Appending a Poly-A Tail to a Reference Transcriptome
bowtie rnaseq ase transcriptome alignment
updated by GenoMax GenoMax • written by jon.klonowski jon.klonowski
0 votes
1 reply
1.8K views
Recovering summit position from ENCODE narrowPeak (BED6+4) format
summit idr peak-calling atac-seq
updated by olivia.doyle • olivia.doyle • written by Ready2Rapture • Ready2Rapture
0 votes
1 reply
1.7K views
Unable to open HDF5 file
hdf5 seurat scrna-seq
updated by bk11 • bk11 • written by Christopher • Christopher
0 votes
2 replies
1.3K views
How to use Diffbind to quantify signal in a set of custom peaks
atac-seq diffbind
written by enanoide • enanoide
0 votes
1 reply
1.8K views
When should I normalize and subset adata objects in scanpy?
scanpy scrna-seq single-cell
updated by LChart LChart • written by bioinfo • bioinfo
0 votes
2 replies
1.4K views
How to Fix "Error in checkForExperimentalReplicates(object, modelMatrix) :"?
deseqdatasetfrommatrix r coldata deseq2 rna-seq
written by thatolivebranch • thatolivebranch
0 votes
4 replies
2.4K views
Wildcards and regular expressions in snakemake
snakemake
updated by tim.booth • tim.booth • written by diop.awa94 • diop.awa94
0 votes
1 reply
1.4K views
AggregateExpression() with return.seurat=TRUE not working as expected
seurat seurat5 aggregateexpression
updated by Bastien Hervé Bastien Hervé • written by BIANCO • BIANCO
0 votes
0 replies
634 views
Checking to see if .hhm file output makes sense
hhblits
updated by GenoMax GenoMax • written by jet • jet
0 votes
1 reply
958 views
Background mutation rate from WGS
mutation-rate snp wgs variant
updated by Ram Ram • written by massa.kassa.sc3na massa.kassa.sc3na
0 votes
1 reply
1.1K views
Fetching records using Entrez
python pubmed entrez
updated by GenoMax GenoMax • written by RAJ • RAJ
0 votes
11 replies
3.1K views
Htseq-count problem with gtf/gff file
htseq
written by Andrea Chiara • Andrea Chiara
0 votes
0 replies
668 views
Generating Protein sequence embeddings from alphafold
llm nlp embedding ai
updated by Ram Ram • written by singhankit973 • singhankit973
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