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0 votes
4 replies
1.5K views
Output checks during Snakemake pipeline
workflow-management snakemake
written by hpapoli hpapoli
0 votes
1 reply
1.4K views
Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
chip-seq quality-check encode library-complexity
written by kalavattam • kalavattam
0 votes
3 replies
1.3K views
Germline variant - should it be seen in the somatic vcf?
vcf somatic
updated by Ram Ram • written by hello_bioinf • hello_bioinf
1 vote
2 replies
1.3K views
How can I Obtain hg38 cancer mutation and variation files
vcf snv variation mutation
updated by gernophil • gernophil • written by kabir.deb • kabir.deb
0 votes
1 reply
1.1K views
Unsupported attributes (CPU/Memory) for pbcromwell workflow manager
cromwell pacbio hgap4
updated by pbioinf • pbioinf • written by Zeng Hao • Zeng Hao
0 votes
2 replies
1.0K views
Padjusted value = 1 in wilcox test
fdr rna-seq wilcox
updated by Ram Ram • written by swathy • swathy
0 votes
1 reply
1.1K views
which haplotypes were saved in .gbz file?
vg
updated by Jouni Sirén Jouni Sirén • written by chuanj8848 • chuanj8848
0 votes
8 replies
2.2K views
Segmentation fault (core dumped)
segmentation-fault blat
updated by Ram Ram • written by isha.lily20 • isha.lily20
0 votes
2 replies
1.2K views
CCA integration
single-cell scrna-seq batch-correction
written by kayah • kayah
0 votes
5 replies
5.0K views
What to consider Bit score or E value
bit_score ngs blastn e_value edna
updated by b.contreras.moreira • b.contreras.moreira • written by koustavroy88 • koustavroy88
0 votes
1 reply
928 views
Autodock Vina not recognizing Chloride ion in ligand.pqbqt file
vina
updated by Mensur Dlakic Mensur Dlakic • written by Sanjukta • Sanjukta
0 votes
1 reply
902 views
reconstruct ecDNA.
plot human ecdna pacbio pbmm2
updated by Pierre Lindenbaum Pierre Lindenbaum • written by María José • María José
0 votes
1 reply
853 views
Empty Results from champ.DMP Despite Expected Output
dmr r champ cpg methylation
updated by Basti • Basti • written by Hiam • Hiam
0 votes
1 reply
678 views
Polymorphic Transposable Elements sequence of Human
polymorphic-transposable-element te 1kgp
updated by Ram Ram • written by Shovan • Shovan
0 votes
0 replies
726 views
Classify SNPs from PacBio data
snps pacbio gex pigeon 10x
written by TheCatalyst • TheCatalyst
0 votes
3 replies
1.3K views
Script for Rstudio
rstudio transcript kallisto analysis
updated by dsull dsull • written by Pumla • Pumla
0 votes
3 replies
1.9K views
blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) databases
kegg kog blast go
updated by Mensur Dlakic Mensur Dlakic • written by Bushra Bibi Bushra Bibi
1 vote
3 replies
2.7K views
GraphAligner/vg surject - alignment output nonsense?
vg-toolkit graphaligner vg vg-surject vgteam
updated by stringsAsBaxters • stringsAsBaxters • written by Andrew • Andrew
0 votes
0 replies
549 views
cuffdiff
cuffdiff
updated by Ram Ram • written by chavanrenuka852 • chavanrenuka852
0 votes
6 replies
2.3K views
If changing the RNA-Seq count normalisation method changes the DGE and downstream analysis results?
tpm normalisation fpm
written by Bushra Bibi Bushra Bibi
7 votes
20 replies
48K views
Generating consensus sequence from bam file
genome samtools bwa fasta
updated by jkbonfield jkbonfield • written by chparada • chparada
0 votes
2 replies
1.3K views
Doublets in scRNAseq analysis
doublet scrnaseq pbmc
written by Binghong • Binghong
0 votes
1 reply
2.1K views
Chemistry Detection Error in CellRanger for Single-Cell RNA-Seq Data
cellranger single-cell rna
updated by GenoMax GenoMax • written by 97sun3 • 97sun3
0 votes
3 replies
1.3K views
DEseq2 with different designs matrix
deseq2
written by QX • QX
0 votes
0 replies
741 views
somatic SV calling with bionano optical mapping data
om sv bionano alignment variants
written by eebloom • eebloom
0 votes
3 replies
1.7K views
I think batch correction didn't working in my dataset(ft. RunHarmony)
scrnaseq
written by kayah • kayah
0 votes
2 replies
1.2K views
Enhanced Volcano not working on ANY data. Coerces everything to NaN
bioconductor enhancedvolcano
updated by Ram Ram • written by Alex • Alex
0 votes
0 replies
645 views
Downstream analysis for CIBERSORTx imputed cell-specific gene expression
cibersortx
updated by Ram Ram • written by Fred Lawrence • Fred Lawrence
0 votes
3 replies
1.6K views
How to represent arbitrarily length kmer?
kmer
written by dwpeng • dwpeng
0 votes
1 reply
855 views
Shift in GC content between forward and reverse reads in ddRADseq data
ddrad sequencing fastqc ddradseq
updated by GenoMax GenoMax • written by Lemonhope • Lemonhope
0 votes
5 replies
2.2K views
No such variable: nextflow
nextflow
updated by Medhat Medhat • written by Mmar • Mmar
0 votes
1 reply
1.5K views
Correct VCF header
vcf
updated by Ram Ram • written by ja569116 • ja569116
0 votes
1 reply
871 views
Need help to figure out what format this SNP calling data is.
snp microarray
updated by GenoMax GenoMax • written by yihangzhu • yihangzhu
0 votes
11 replies
2.6K views
Differential gene expression
deseq2 differential gene expression
updated by OmnibusX • OmnibusX • written by 4732b159 • 4732b159
0 votes
4 replies
2.3K views
Microbial pathway analysis tool or pipeline
pathways 16srrna microbiome
written by ssko • ssko
0 votes
0 replies
640 views
Different SNPs found: WGS aligned to WES
wes alignment wgs
written by ramiro.barrantes • ramiro.barrantes
0 votes
1 reply
1.6K views
Updating phenotype column for .ped .fam files (PLINK --pheno not working)
phenotype plink --pheno gwas binary
updated by bk11 • bk11 • written by sabrilo171 • sabrilo171
0 votes
0 replies
584 views
Handling FILTER Fields in VCF Metadata and Body
vcf
written by ManuelDB ManuelDB
0 votes
0 replies
864 views
DESeq2 Install in Jupyter Notebook
deseq2 jupyter
updated by Ram Ram • written by Lolo • Lolo
0 votes
1 reply
951 views
Controlling for Baseline Taxa Relative Abundance [Longitudinal 16S rRNA Sequencing Data]
qiime 16srrna sequencing ancombc-2
written by bjeremy • bjeremy
0 votes
2 replies
1.3K views
Using findmarker of seurat with different test.use but getting the same resulat.
seurat
updated by bk11 • bk11 • written by Sep • Sep
0 votes
7 replies
4.1K views
Core_nt database not available to download?
blast ncbi
updated by GenoMax GenoMax • written by DNAngel DNAngel
0 votes
0 replies
736 views
News: Course in Italy: Introduction to Statistics in R (30 September to 3 October 2024)
r glm statistics glmm
written by Physalia-courses Physalia-courses
1 vote
3 replies
1.4K views
Rapid K-mer search
search k-mer
updated by shenwei356 shenwei356 • written by Anjan Anjan
0 votes
2 replies
1.0K views
Restrictive alignment with minimap2
nanopore alignment minimap2
written by njornet • njornet
0 votes
1 reply
945 views
TPM normalization of counts
tpm featurecounts
written by Bushra Bibi Bushra Bibi
0 votes
4 replies
1.7K views
Nr Database just for Prokaryotes
nr database
updated by GenoMax GenoMax • written by echolley • echolley
0 votes
0 replies
555 views
I encounter a problem while checking my MaGeck results.
mageck
written by Pallondyle • Pallondyle
0 votes
7 replies
2.5K views
How to check coverage in bam file?
bam
updated by cmdcolin cmdcolin • written by shinyjj • shinyjj
0 votes
0 replies
560 views
DiffBind for MBD-seq
diffbind mbd-seq
written by mariannapauletto • mariannapauletto
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