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0 votes
1 reply
2.0K views
Treemix is taking too long running
treemix cutadapt ubuntu
updated by Michael Dondrup Michael Dondrup • written by Camila Martínez • Camila Martínez
0 votes
4 replies
1.8K views
can someone please explain the DAPARS output?
rna-seq apa dapars2
written by PK • PK
0 votes
7 replies
2.2K views
How to create a tax_id_map file for getting scientific names in BLASTN output
blast ncbi
written by Maria • Maria
0 votes
0 replies
483 views
What to do with ALDEx2 associations where p < 0.05, but the 95% confidence intervals bridge zero
metagenomics aldex2 differential-abundance
updated by Ram Ram • written by Sam • Sam
0 votes
2 replies
970 views
low ribosomal protein in scrnaseq data
ribosomal-proteins scrna-seq
updated by Ram Ram • written by hemnes.boston.87 • hemnes.boston.87
0 votes
1 reply
1.1K views
Redundant Database for BLAST search
database taxonomy phylogeny blast
updated by GenoMax GenoMax • written by Emily • Emily
0 votes
1 reply
992 views
Should mutations in repetitive base positions be considered real
cancer dna
updated by Joe Joe • written by tan • tan
0 votes
1 reply
1.4K views
Extracting Enhancer Regions from ENCODE Annotation Files
encode enhancer
updated by Alexandra • Alexandra • written by YamengWu • YamengWu
0 votes
3 replies
1.5K views
VG - Verifying presence or absence of variants in Pangenome Graph
mutation variant pangenome vcf vg
updated by Jordan M Eizenga • Jordan M Eizenga • written by nkls063408 • nkls063408
0 votes
0 replies
2.0K views
Using get_normalized_expression (scVI) vs. Log-Normalized Counts
scvi normalization rna-seq single-cell umap
written by Nicolas • Nicolas
0 votes
1 reply
678 views
Collapse technical replicates in DEGS
rna-seq degs technical-replicates
updated by Ram Ram • written by drajangirija • drajangirija
0 votes
2 replies
1.0K views
Time-series statistics for a small amount of genes
rna-seq time-series
written by Aspire Aspire
0 votes
0 replies
606 views
News: Course - Introduction to R Shiny
r web-applications shiny
written by Physalia-courses Physalia-courses
0 votes
8 replies
2.6K views
minimap2 for polyA site sequenced with long read data (both cDNA ONT, PacBio)
minimap2
written by shinyjj • shinyjj
0 votes
1 reply
783 views
Isoforms and Transcriptome assembly with direct RNA Nanopore reads
isoforms assembly transcriptome sequencing nanopore
updated by GenoMax GenoMax • written by mariana.villegas • mariana.villegas
2 votes
11 replies
6.9K views
Randomly select a number of variants and samples from a multi-sample VCF file (pVCF)
vcf pvcf
updated by Michael Dondrup Michael Dondrup • written by ' '
0 votes
7 replies
2.9K views
Need to split a cram file into smaller pieces - how to extract and save cram format to a new file?
samtools cram
updated by weisburd • weisburd • written by Ann Ann
0 votes
3 replies
1.1K views
Hybrid assembly with Unicycler and multiple files of input
unicycler assembly
updated by shelkmike shelkmike • written by langziv • langziv
0 votes
3 replies
1.3K views
What should I use correlate/compare microbiome compositional data to other data types
r python microbiome compositional-biology
updated by dthorbur dthorbur • written by Faith • Faith
0 votes
0 replies
702 views
How to Accurately Determine Unique Mapped Reads from HISAT2 Output summary file
mapped unique analysis hisat2 rna-seq
updated by GenoMax GenoMax • written by Nelo • Nelo
0 votes
0 replies
524 views
News: Course: Advance your Python Skills for Life Sciences
python vpython pythonlang
updated by Ram Ram • written by Transmitting Science communication • Transmitting Science communication
0 votes
0 replies
569 views
News: Course: Introduction to R
rproject rlang rstats
updated by Ram Ram • written by Transmitting Science communication • Transmitting Science communication
1 vote
2 replies
1.5K views
R package to visualize multiple aligned chromatograms
r plot chromatogram sanger
written by DaniCee • DaniCee
0 votes
3 replies
1.3K views
issue with terms label in Go dotplots
r clusterprofiler go-terms
written by G.S • G.S
0 votes
0 replies
573 views
BCftools call when using -v -V indels vs using -V indels only
bcftools plink
written by Jimmy M • Jimmy M
0 votes
5 replies
1.6K views
How to make the length of the CDS of my bed file divisible by 3?
annotation cds toga bed
updated by Michael Dondrup Michael Dondrup • written by blumina.r • blumina.r
0 votes
0 replies
751 views
News: Course: Introduction to the Analysis of Longitudinal Data in Biology Using R
longitudinal-data r epidemiology forecasting gene-expression
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
8 replies
2.7K views
p-value/adjusted p-vlaue cutoff
adjusted-pvalue p-value deseq2 fgsea
updated by Jean-Karim Heriche Jean-Karim Heriche • written by alex.kang1014 • alex.kang1014
0 votes
1 reply
1.1K views
bamCoverage - how BPM normalization was done?
bamcoverage chip-seq deeptools
written by Pei Pei
0 votes
0 replies
491 views
Help needed to troubleshoot : conversion error with open babel on cmd
open-babel
updated by Ram Ram • written by Sanjukta • Sanjukta
0 votes
0 replies
633 views
No MAF filtering for GWAS
gwas
updated by Ram Ram • written by K Lee • K Lee
0 votes
4 replies
1.5K views
DNA SPRITE Expirment Benchmark
sprite genome
updated by Ram Ram • written by Amaal • Amaal
0 votes
5 replies
2.0K views
Centrifuge Index creation issue
metagenomics centrifuge
written by skbrimer skbrimer
0 votes
6 replies
2.0K views
Non-existent transcript as a result from Salmon
rnaseq salmon
written by Vojtěch • Vojtěch
1 vote
1 reply
1.1K views
How to calculate differentially spliced genes in single cell?
scrna velocyto splicing scvelo
updated by ATpoint ATpoint • written by zeina • zeina
0 votes
2 replies
935 views
Basic coding-Stuck with Java script while working with KNIME
java
written by Sanjukta • Sanjukta
2 votes
2 replies
1.3K views
How can we determine or find the insertion time of Numts?
pacbio bioinformatician mtdna numts
written by hashim.rana11 • hashim.rana11
1 vote
5 replies
5.0K views
Differential expression Analysis of PacBio Isoseq data
differential-expression-analysis isoseq
written by tvibhaps • tvibhaps
0 votes
1 reply
899 views
Book about RNA structure
rna
updated by Mensur Dlakic Mensur Dlakic • written by bef1 • bef1
0 votes
2 replies
947 views
eagle: error: argument command: invalid choice: 'DATASET_chr_for_phasing.vcf.gz' (choose from 'interface', 'convert')
gwas-imputation
written by nareshmvr • nareshmvr
0 votes
0 replies
768 views
whatshap ploidy error on female sample
ont ploidy phasing nanopore
updated by Ram Ram • written by eebloom • eebloom
0 votes
0 replies
705 views
ROSE analysis is empty
chip-seq h3k27ac rose
written by pb11 • pb11
1 vote
0 replies
565 views
Seeking Advice on Protein Evidence for GALBA Annotation of Non-Model Rodent Genome
annotation galba maker genome breaker
written by aleponce • aleponce
0 votes
4 replies
3.2K views
difference between macs2 callpeak using bam and bed file
macs2 atac-seq
written by QX • QX
0 votes
1 reply
798 views
Reference source that provides IRIs for Ensembl gene IDs?
ensembl iri
updated by GenoMax GenoMax • written by nkabo nkabo
0 votes
1 reply
1.1K views
Can i use population as a trait to perform GWAS?
hapmap plink gwas qc
updated by dthorbur dthorbur • written by Yugan Gogul Muthukumar • Yugan Gogul Muthukumar
0 votes
15 replies
4.9K views
How to give 2 input files (one from the process before and one from 3 processes before) in nextflow pipeline?
nextflow nf-core processes channels
updated by colindaven colindaven • written by giulia.trauzzi • giulia.trauzzi
0 votes
0 replies
570 views
Should I plot with methylDiff or methylBase object?
methylkit
written by CTLong • CTLong
0 votes
5 replies
2.5K views
Differential gene expression (aiming to create heatmap) for raw RNAseq count data from different publications - how to?
r deseq2 differential-expression
updated by BioinfGuru BioinfGuru • written by Leah • Leah
1 vote
18 replies
5.4K views
Forum: Is "training", fine tuning, or overfitting on "external independent validation datasets" considered cheating or scientific misconduct?
tools scientific misconduct overfitting
written by ivicts • ivicts
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